3CEP

Structure of a tryptophan synthase quinonoid intermediate

PDB DOI: https://doi.org/10.2210/pdb3CEP/pdb

Classification: LYASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-29 Released: 2008-04-01
Deposition Author(s): Barends, T.R.M., Domratcheva, T., Kulik, V., Blumenstein, L., Dunn, M.F., Schlichting, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 ?
R-Value Free: 0.238
R-Value Work: 0.198
R-Value Observed: 0.200

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure and mechanistic implications of a tryptophan synthase quinonoid intermediate.

Barends, T.R., Domratcheva, T., Kulik, V., Blumenstein, L., Niks, D., Dunn, M.F., Schlichting, I.

(2008) Chembiochem 9: 1024-1028

PubMed: 18351684 Search on PubMed
DOI: https://doi.org/10.1002/cbic.200700703
Primary Citation of Related Structures:
3CEP

Organizational Affiliation

Abteilung Biomolekulare Mechanismen, Max Planck Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.

Macromolecule Content

Total Structure Weight: 72.65 kDa
Atom Count: 5,266
Modelled Residue Count: 659
Deposited Residue Count: 664
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase alpha chain	A	268	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: trpA EC: 4.2.1.20
UniProt
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P00929 Go to UniProtKB: P00929
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00929
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain	B	396	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: trpB EC: 4.2.1.20
UniProt
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A2K1 Go to UniProtKB: P0A2K1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A2K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
G3P Query on G3P Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SN-GLYCEROL-3-PHOSPHATE C₃ H₉ O₆ P AWUCVROLDVIAJX-GSVOUGTGSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CS Query on CS Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	E [auth B], F [auth B], G [auth B]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B]
IDM Query on IDM Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	INDOLINE C₈ H₉ N LPAGFVYQRIESJQ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
MH6 Query on MH6 Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	3-hydroxy-2-iminopropanoic acid C₃ H₅ N O₃ MUHXUPVPXJXCGV-DUXPYHPUSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 ?
R-Value Free: 0.238
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: C 1 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 184.024	α = 90
b = 58.908	β = 95.19
c = 67.086	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-04-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-04-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2014-12-17
Changes: Experimental preparation
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

3CEP

Structure of a tryptophan synthase quinonoid intermediate

Structure and mechanistic implications of a tryptophan synthase quinonoid intermediate.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2