7Q9Z | pdb_00007q9z

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

PDB DOI: https://doi.org/10.2210/pdb7Q9Z/pdb

Classification: TRANSFERASE
Organism(s): Chromobacterium violaceum ATCC 12472
Expression System: Escherichia coli BL21(DE3)
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: 1.95 ?
R-Value Free:
0.279 (Depositor), 0.280 (DCC)
R-Value Work:
0.243 (Depositor), 0.240 (DCC)

Starting Model: experimental
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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: 110.69 kDa
Atom Count: 6,881
Modelled Residue Count: 854
Deposited Residue Count: 986
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable aminotransferase	A [auth AAA], B [auth BBB]	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 4 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 C [auth AAA] SDF format, chain H [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain H [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain H [auth BBB]	C [auth AAA], H [auth BBB]	(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 C [auth AAA] Focus chain H [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain H [auth BBB]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain I [auth BBB] SDF format, chain J [auth BBB] SDF format, chain K [auth BBB] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain I [auth BBB] MOL2 format, chain J [auth BBB] MOL2 format, chain K [auth BBB] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain I [auth BBB] mmCIF format, chain J [auth BBB] mmCIF format, chain K [auth BBB]	D [auth AAA], E [auth AAA], I [auth BBB], J [auth BBB], K [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain I [auth BBB] Focus chain J [auth BBB] Focus chain K [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain I [auth BBB] Focus chain J [auth BBB] Focus chain K [auth BBB]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth AAA] Interactions & Density Focus chain F [auth AAA]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain L [auth BBB] MOL2 format, chain G [auth AAA] MOL2 format, chain L [auth BBB] mmCIF format, chain G [auth AAA] mmCIF format, chain L [auth BBB]	G [auth AAA], L [auth BBB]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Focus chain L [auth BBB] Interactions & Density Focus chain G [auth AAA] Focus chain L [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 ?
R-Value Free: 0.279 (Depositor), 0.280 (DCC)
R-Value Work: 0.243 (Depositor), 0.240 (DCC)

Space Group: P 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 58.15	α = 71.3
b = 60.72	β = 75.94
c = 61.8	γ = 85.73

Software Package:

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

Structure Validation

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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