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.

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Experimental Data Snapshot

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

Starting Model: experimental

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 
• DOI: https://doi.org/10.1002/cbic.200700703
• Primary Citation of Related Structures:  
  3CEP

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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 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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	H [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
G3P	C [auth A]	SN-GLYCEROL-3-PHOSPHATE C3 H9 O6 P AWUCVROLDVIAJX-GSVOUGTGSA-N
CS	E [auth B], F [auth B], G [auth B]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N
IDM	D [auth A], J [auth B]	INDOLINE C8 H9 N LPAGFVYQRIESJQ-UHFFFAOYSA-N
MH6	I [auth B]	3-hydroxy-2-iminopropanoic acid C3 H5 N O3 MUHXUPVPXJXCGV-DUXPYHPUSA-N

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length ( Å )	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

Entry History 

Deposition Data

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

Revision History  

• 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