7Q9X | pdb_00007q9x

Crystal structure of Chromobacterium violaceum aminotransferase in complex with PLP-pyruvate adduct

PDB DOI: https://doi.org/10.2210/pdb7Q9X/pdb

Classification: TRANSFERASE
Organism(s): Chromobacterium violaceum ATCC 12472
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-11-15 Released: 2022-11-23
Deposition Author(s): Isupov, M.N., Mitchell, D., Sayer, C., Littlechild, J.A.
Funding Organization(s): Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 ?
R-Value Free:
0.261 (Depositor), 0.260 (DCC)
R-Value Work:
0.227 (Depositor), 0.230 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Aminotransferase from Chromobacterium violaceum in complex with PLP-pyruvate adduct.

Isupov, M.N., Mitchell, D., Sayer, C., Littlechild, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 223.22 kDa
Atom Count: 17,188
Modelled Residue Count: 1,820
Deposited Residue Count: 1,972
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable aminotransferase	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	493	Chromobacterium violaceum ATCC 12472	Mutation(s): 0 Gene Names: CV_2025 EC: 2.6.1.62
UniProt
Find proteins for Q7NWG4 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NWG4 Go to UniProtKB: Q7NWG4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7NWG4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AN7 (Subject of Investigation/LOI) Query on AN7 Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain SB [auth DDD] SDF format, chain U [auth BBB] SDF format, chain YA [auth CCC] MOL2 format, chain E [auth AAA] MOL2 format, chain SB [auth DDD] MOL2 format, chain U [auth BBB] MOL2 format, chain YA [auth CCC] mmCIF format, chain E [auth AAA] mmCIF format, chain SB [auth DDD] mmCIF format, chain U [auth BBB] mmCIF format, chain YA [auth CCC]	E [auth AAA], SB [auth DDD], U [auth BBB], YA [auth CCC]	(3E)-4-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}-2-oxobut-3-enoic acid C₁₁ H₁₂ N O₈ P FYMYHYJKCICXRI-NSCUHMNNSA-N		Interactions Focus chain E [auth AAA] Focus chain SB [auth DDD] Focus chain U [auth BBB] Focus chain YA [auth CCC] Interactions & Density Focus chain E [auth AAA] Focus chain SB [auth DDD] Focus chain U [auth BBB] Focus chain YA [auth CCC]
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain W [auth BBB] MOL2 format, chain W [auth BBB] mmCIF format, chain W [auth BBB]	W [auth BBB]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain W [auth BBB] Interactions & Density Focus chain W [auth BBB]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain ZA [auth CCC] MOL2 format, chain ZA [auth CCC] mmCIF format, chain ZA [auth CCC]	ZA [auth CCC]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain ZA [auth CCC] Interactions & Density Focus chain ZA [auth CCC]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain UB [auth DDD] SDF format, chain X [auth BBB] MOL2 format, chain UB [auth DDD] MOL2 format, chain X [auth BBB] mmCIF format, chain UB [auth DDD] mmCIF format, chain X [auth BBB]	UB [auth DDD], X [auth BBB]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain UB [auth DDD] Focus chain X [auth BBB] Interactions & Density Focus chain UB [auth DDD] Focus chain X [auth BBB]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth CCC] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain TB [auth DDD] SDF format, chain V [auth BBB] MOL2 format, chain AB [auth CCC] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain TB [auth DDD] MOL2 format, chain V [auth BBB] mmCIF format, chain AB [auth CCC] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain TB [auth DDD] mmCIF format, chain V [auth BBB]	AB [auth CCC], F [auth AAA], G [auth AAA], TB [auth DDD], V [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth CCC] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain TB [auth DDD] Focus chain V [auth BBB] Interactions & Density Focus chain AB [auth CCC] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain TB [auth DDD] Focus chain V [auth BBB]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth BBB] SDF format, chain AC [auth DDD] SDF format, chain BA [auth BBB] SDF format, chain BB [auth CCC] SDF format, chain BC [auth DDD] SDF format, chain CA [auth BBB] SDF format, chain CB [auth CCC] SDF format, chain CC [auth DDD] SDF format, chain DA [auth BBB] SDF format, chain DB [auth CCC] SDF format, chain DC [auth DDD] SDF format, chain EA [auth BBB] SDF format, chain EB [auth CCC] SDF format, chain EC [auth DDD] SDF format, chain FA [auth BBB] SDF format, chain FB [auth CCC] SDF format, chain FC [auth DDD] SDF format, chain GA [auth BBB] SDF format, chain GB [auth CCC] SDF format, chain GC [auth DDD] SDF format, chain H [auth AAA] SDF format, chain HA [auth BBB] SDF format, chain HB [auth CCC] SDF format, chain HC [auth DDD] SDF format, chain I [auth AAA] SDF format, chain IA [auth BBB] SDF format, chain IB [auth CCC] SDF format, chain IC [auth DDD] SDF format, chain J [auth AAA] SDF format, chain JA [auth BBB] SDF format, chain JB [auth CCC] SDF format, chain JC [auth DDD] SDF format, chain K [auth AAA] SDF format, chain KA [auth BBB] SDF format, chain KB [auth CCC] SDF format, chain KC [auth DDD] SDF format, chain L [auth AAA] SDF format, chain LA [auth BBB] SDF format, chain LB [auth CCC] SDF format, chain LC [auth DDD] SDF format, chain M [auth AAA] SDF format, chain MA [auth BBB] SDF format, chain MB [auth CCC] SDF format, chain MC [auth DDD] SDF format, chain N [auth AAA] SDF format, chain NA [auth BBB] SDF format, chain NB [auth CCC] SDF format, chain NC [auth DDD] SDF format, chain O [auth AAA] SDF format, chain OA [auth BBB] SDF format, chain OB [auth CCC] SDF format, chain OC [auth DDD] SDF format, chain P [auth AAA] SDF format, chain PA [auth BBB] SDF format, chain PB [auth CCC] SDF format, chain PC [auth DDD] SDF format, chain Q [auth AAA] SDF format, chain QA [auth BBB] SDF format, chain QB [auth CCC] SDF format, chain R [auth AAA] SDF format, chain RA [auth BBB] SDF format, chain RB [auth CCC] SDF format, chain S [auth AAA] SDF format, chain SA [auth BBB] SDF format, chain T [auth AAA] SDF format, chain TA [auth BBB] SDF format, chain UA [auth BBB] SDF format, chain VA [auth BBB] SDF format, chain VB [auth DDD] SDF format, chain WA [auth BBB] SDF format, chain WB [auth DDD] SDF format, chain XA [auth BBB] SDF format, chain XB [auth DDD] SDF format, chain Y [auth BBB] SDF format, chain YB [auth DDD] SDF format, chain Z [auth BBB] SDF format, chain ZB [auth DDD] MOL2 format, chain AA [auth BBB] MOL2 format, chain AC [auth DDD] MOL2 format, chain BA [auth BBB] MOL2 format, chain BB [auth CCC] MOL2 format, chain BC [auth DDD] MOL2 format, chain CA [auth BBB] MOL2 format, chain CB [auth CCC] MOL2 format, chain CC [auth DDD] MOL2 format, chain DA [auth BBB] MOL2 format, chain DB [auth CCC] MOL2 format, chain DC [auth DDD] MOL2 format, chain EA [auth BBB] MOL2 format, chain EB [auth CCC] MOL2 format, chain EC [auth DDD] MOL2 format, chain FA [auth BBB] MOL2 format, chain FB [auth CCC] MOL2 format, chain FC [auth DDD] MOL2 format, chain GA [auth BBB] MOL2 format, chain GB [auth CCC] MOL2 format, chain GC [auth DDD] MOL2 format, chain H [auth AAA] MOL2 format, chain HA [auth BBB] MOL2 format, chain HB [auth CCC] MOL2 format, chain HC [auth DDD] MOL2 format, chain I [auth AAA] MOL2 format, chain IA [auth BBB] MOL2 format, chain IB [auth CCC] MOL2 format, chain IC [auth DDD] MOL2 format, chain J [auth AAA] MOL2 format, chain JA [auth BBB] MOL2 format, chain JB [auth CCC] MOL2 format, chain JC [auth DDD] MOL2 format, chain K [auth AAA] MOL2 format, chain KA [auth BBB] MOL2 format, chain KB [auth CCC] MOL2 format, chain KC [auth DDD] MOL2 format, chain L [auth AAA] MOL2 format, chain LA [auth BBB] MOL2 format, chain LB [auth CCC] MOL2 format, chain LC [auth DDD] MOL2 format, chain M [auth AAA] MOL2 format, chain MA [auth BBB] MOL2 format, chain MB [auth CCC] MOL2 format, chain MC [auth DDD] MOL2 format, chain N [auth AAA] MOL2 format, chain NA [auth BBB] MOL2 format, chain NB [auth CCC] MOL2 format, chain NC [auth DDD] MOL2 format, chain O [auth AAA] MOL2 format, chain OA [auth BBB] MOL2 format, chain OB [auth CCC] MOL2 format, chain OC [auth DDD] MOL2 format, chain P [auth AAA] MOL2 format, chain PA [auth BBB] MOL2 format, chain PB [auth CCC] MOL2 format, chain PC [auth DDD] MOL2 format, chain Q [auth AAA] MOL2 format, chain QA [auth BBB] MOL2 format, chain QB [auth CCC] MOL2 format, chain R [auth AAA] MOL2 format, chain RA [auth BBB] MOL2 format, chain RB [auth CCC] MOL2 format, chain S [auth AAA] MOL2 format, chain SA [auth BBB] MOL2 format, chain T [auth AAA] MOL2 format, chain TA [auth BBB] MOL2 format, chain UA [auth BBB] MOL2 format, chain VA [auth BBB] MOL2 format, chain VB [auth DDD] MOL2 format, chain WA [auth BBB] MOL2 format, chain WB [auth DDD] MOL2 format, chain XA [auth BBB] MOL2 format, chain XB [auth DDD] MOL2 format, chain Y [auth BBB] MOL2 format, chain YB [auth DDD] MOL2 format, chain Z [auth BBB] MOL2 format, chain ZB [auth DDD] mmCIF format, chain AA [auth BBB] mmCIF format, chain AC [auth DDD] mmCIF format, chain BA [auth BBB] mmCIF format, chain BB [auth CCC] mmCIF format, chain BC [auth DDD] mmCIF format, chain CA [auth BBB] mmCIF format, chain CB [auth CCC] mmCIF format, chain CC [auth DDD] mmCIF format, chain DA [auth BBB] mmCIF format, chain DB [auth CCC] mmCIF format, chain DC [auth DDD] mmCIF format, chain EA [auth BBB] mmCIF format, chain EB [auth CCC] mmCIF format, chain EC [auth DDD] mmCIF format, chain FA [auth BBB] mmCIF format, chain FB [auth CCC] mmCIF format, chain FC [auth DDD] mmCIF format, chain GA [auth BBB] mmCIF format, chain GB [auth CCC] mmCIF format, chain GC [auth DDD] mmCIF format, chain H [auth AAA] mmCIF format, chain HA [auth BBB] mmCIF format, chain HB [auth CCC] mmCIF format, chain HC [auth DDD] mmCIF format, chain I [auth AAA] mmCIF format, chain IA [auth BBB] mmCIF format, chain IB [auth CCC] mmCIF format, chain IC [auth DDD] mmCIF format, chain J [auth AAA] mmCIF format, chain JA [auth BBB] mmCIF format, chain JB [auth CCC] mmCIF format, chain JC [auth DDD] mmCIF format, chain K [auth AAA] mmCIF format, chain KA [auth BBB] mmCIF format, chain KB [auth CCC] mmCIF format, chain KC [auth DDD] mmCIF format, chain L [auth AAA] mmCIF format, chain LA [auth BBB] mmCIF format, chain LB [auth CCC] mmCIF format, chain LC [auth DDD] mmCIF format, chain M [auth AAA] mmCIF format, chain MA [auth BBB] mmCIF format, chain MB [auth CCC] mmCIF format, chain MC [auth DDD] mmCIF format, chain N [auth AAA] mmCIF format, chain NA [auth BBB] mmCIF format, chain NB [auth CCC] mmCIF format, chain NC [auth DDD] mmCIF format, chain O [auth AAA] mmCIF format, chain OA [auth BBB] mmCIF format, chain OB [auth CCC] mmCIF format, chain OC [auth DDD] mmCIF format, chain P [auth AAA] mmCIF format, chain PA [auth BBB] mmCIF format, chain PB [auth CCC] mmCIF format, chain PC [auth DDD] mmCIF format, chain Q [auth AAA] mmCIF format, chain QA [auth BBB] mmCIF format, chain QB [auth CCC] mmCIF format, chain R [auth AAA] mmCIF format, chain RA [auth BBB] mmCIF format, chain RB [auth CCC] mmCIF format, chain S [auth AAA] mmCIF format, chain SA [auth BBB] mmCIF format, chain T [auth AAA] mmCIF format, chain TA [auth BBB] mmCIF format, chain UA [auth BBB] mmCIF format, chain VA [auth BBB] mmCIF format, chain VB [auth DDD] mmCIF format, chain WA [auth BBB] mmCIF format, chain WB [auth DDD] mmCIF format, chain XA [auth BBB] mmCIF format, chain XB [auth DDD] mmCIF format, chain Y [auth BBB] mmCIF format, chain YB [auth DDD] mmCIF format, chain Z [auth BBB] mmCIF format, chain ZB [auth DDD]	AA [auth BBB] AC [auth DDD] BA [auth BBB] BB [auth CCC] BC [auth DDD] AA [auth BBB], AC [auth DDD], BA [auth BBB], BB [auth CCC], BC [auth DDD], CA [auth BBB], CB [auth CCC], CC [auth DDD], DA [auth BBB], DB [auth CCC], DC [auth DDD], EA [auth BBB], EB [auth CCC], EC [auth DDD], FA [auth BBB], FB [auth CCC], FC [auth DDD], GA [auth BBB], GB [auth CCC], GC [auth DDD], H [auth AAA], HA [auth BBB], HB [auth CCC], HC [auth DDD], I [auth AAA], IA [auth BBB], IB [auth CCC], IC [auth DDD], J [auth AAA], JA [auth BBB], JB [auth CCC], JC [auth DDD], K [auth AAA], KA [auth BBB], KB [auth CCC], KC [auth DDD], L [auth AAA], LA [auth BBB], LB [auth CCC], LC [auth DDD], M [auth AAA], MA [auth BBB], MB [auth CCC], MC [auth DDD], N [auth AAA], NA [auth BBB], NB [auth CCC], NC [auth DDD], O [auth AAA], OA [auth BBB], OB [auth CCC], OC [auth DDD], P [auth AAA], PA [auth BBB], PB [auth CCC], PC [auth DDD], Q [auth AAA], QA [auth BBB], QB [auth CCC], R [auth AAA], RA [auth BBB], RB [auth CCC], S [auth AAA], SA [auth BBB], T [auth AAA], TA [auth BBB], UA [auth BBB], VA [auth BBB], VB [auth DDD], WA [auth BBB], WB [auth DDD], XA [auth BBB], XB [auth DDD], Y [auth BBB], YB [auth DDD], Z [auth BBB], ZB [auth DDD]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth BBB] Focus chain AC [auth DDD] Focus chain BA [auth BBB] Focus chain BB [auth CCC] Focus chain BC [auth DDD] Focus chain CA [auth BBB] Focus chain CB [auth CCC] Focus chain CC [auth DDD] Focus chain DA [auth BBB] Focus chain DB [auth CCC] Focus chain DC [auth DDD] Focus chain EA [auth BBB] Focus chain EB [auth CCC] Focus chain EC [auth DDD] Focus chain FA [auth BBB] Focus chain FB [auth CCC] Focus chain FC [auth DDD] Focus chain GA [auth BBB] Focus chain GB [auth CCC] Focus chain GC [auth DDD] Focus chain H [auth AAA] Focus chain HA [auth BBB] Focus chain HB [auth CCC] Focus chain HC [auth DDD] Focus chain I [auth AAA] Focus chain IA [auth BBB] Focus chain IB [auth CCC] Focus chain IC [auth DDD] Focus chain J [auth AAA] Focus chain JA [auth BBB] Focus chain JB [auth CCC] Focus chain JC [auth DDD] Focus chain K [auth AAA] Focus chain KA [auth BBB] Focus chain KB [auth CCC] Focus chain KC [auth DDD] Focus chain L [auth AAA] Focus chain LA [auth BBB] Focus chain LB [auth CCC] Focus chain LC [auth DDD] Focus chain M [auth AAA] Focus chain MA [auth BBB] Focus chain MB [auth CCC] Focus chain MC [auth DDD] Focus chain N [auth AAA] Focus chain NA [auth BBB] Focus chain NB [auth CCC] Focus chain NC [auth DDD] Focus chain O [auth AAA] Focus chain OA [auth BBB] Focus chain OB [auth CCC] Focus chain OC [auth DDD] Focus chain P [auth AAA] Focus chain PA [auth BBB] Focus chain PB [auth CCC] Focus chain PC [auth DDD] Focus chain Q [auth AAA] Focus chain QA [auth BBB] Focus chain QB [auth CCC] Focus chain R [auth AAA] Focus chain RA [auth BBB] Focus chain RB [auth CCC] Focus chain S [auth AAA] Focus chain SA [auth BBB] Focus chain T [auth AAA] Focus chain TA [auth BBB] Focus chain UA [auth BBB] Focus chain VA [auth BBB] Focus chain VB [auth DDD] Focus chain WA [auth BBB] Focus chain WB [auth DDD] Focus chain XA [auth BBB] Focus chain XB [auth DDD] Focus chain Y [auth BBB] Focus chain YB [auth DDD] Focus chain Z [auth BBB] Focus chain ZB [auth DDD] Interactions & Density Focus chain AA [auth BBB] Focus chain AC [auth DDD] Focus chain BA [auth BBB] Focus chain BB [auth CCC] Focus chain BC [auth DDD] Focus chain CA [auth BBB] Focus chain CB [auth CCC] Focus chain CC [auth DDD] Focus chain DA [auth BBB] Focus chain DB [auth CCC] Focus chain DC [auth DDD] Focus chain EA [auth BBB] Focus chain EB [auth CCC] Focus chain EC [auth DDD] Focus chain FA [auth BBB] Focus chain FB [auth CCC] Focus chain FC [auth DDD] Focus chain GA [auth BBB] Focus chain GB [auth CCC] Focus chain GC [auth DDD] Focus chain H [auth AAA] Focus chain HA [auth BBB] Focus chain HB [auth CCC] Focus chain HC [auth DDD] Focus chain I [auth AAA] Focus chain IA [auth BBB] Focus chain IB [auth CCC] Focus chain IC [auth DDD] Focus chain J [auth AAA] Focus chain JA [auth BBB] Focus chain JB [auth CCC] Focus chain JC [auth DDD] Focus chain K [auth AAA] Focus chain KA [auth BBB] Focus chain KB [auth CCC] Focus chain KC [auth DDD] Focus chain L [auth AAA] Focus chain LA [auth BBB] Focus chain LB [auth CCC] Focus chain LC [auth DDD] Focus chain M [auth AAA] Focus chain MA [auth BBB] Focus chain MB [auth CCC] Focus chain MC [auth DDD] Focus chain N [auth AAA] Focus chain NA [auth BBB] Focus chain NB [auth CCC] Focus chain NC [auth DDD] Focus chain O [auth AAA] Focus chain OA [auth BBB] Focus chain OB [auth CCC] Focus chain OC [auth DDD] Focus chain P [auth AAA] Focus chain PA [auth BBB] Focus chain PB [auth CCC] Focus chain PC [auth DDD] Focus chain Q [auth AAA] Focus chain QA [auth BBB] Focus chain QB [auth CCC] Focus chain R [auth AAA] Focus chain RA [auth BBB] Focus chain RB [auth CCC] Focus chain S [auth AAA] Focus chain SA [auth BBB] Focus chain T [auth AAA] Focus chain TA [auth BBB] Focus chain UA [auth BBB] Focus chain VA [auth BBB] Focus chain VB [auth DDD] Focus chain WA [auth BBB] Focus chain WB [auth DDD] Focus chain XA [auth BBB] Focus chain XB [auth DDD] Focus chain Y [auth BBB] Focus chain YB [auth DDD] Focus chain Z [auth BBB] Focus chain ZB [auth DDD]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 ?
R-Value Free: 0.261 (Depositor), 0.260 (DCC)
R-Value Work: 0.227 (Depositor), 0.230 (DCC)

Space Group: P 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 60.33	α = 103.56
b = 61.38	β = 89.38
c = 116.48	γ = 105.42

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
DM	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/T002875/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/L002035/1