2OPJ | pdb_00002opj

Crystal structure of O-succinylbenzoate synthase

• PDB DOI: https://doi.org/10.2210/pdb2OPJ/pdb

• Classification: LYASE
• Organism(s): Thermobifida fusca YX
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-01-29 Released: 2007-02-20 
• Deposition Author(s): Sugadev, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Crystal structure of O-succinylbenzoate synthase

Sugadev, R., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.5 kDa 
• Atom Count: 2,416 
• Modeled Residue Count: 294 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-succinylbenzoate-CoA synthase	A	327	Thermobifida fusca YX	Mutation(s): 2  Gene Names: Tfu_1410 EC: 4.2.1 (PDB Primary Data), 4.2.1.113 (UniProt)
UniProt
Find proteins for Q47Q21 (Thermobifida fusca (strain YX)) Explore Q47Q21  Go to UniProtKB:  Q47Q21

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.976	α = 71.28
b = 37.642	β = 76.13
c = 51.99	γ = 73.23

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-20 
Deposition Author(s): Sugadev, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-02-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references
• Version 1.5: 2024-11-06
  Changes: Structure summary