2C6X | pdb_00002c6x

Structure of Bacillus subtilis citrate synthase

• PDB DOI: https://doi.org/10.2210/pdb2C6X/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-11-14 Released: 2007-06-26 
• Deposition Author(s): Vogl, C., Hough, D.W., Danson, M.J., Crennell, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.316 (Depositor), 0.299 (DCC) 
• R-Value Work: 
  0.284 (Depositor), 0.269 (DCC) 
• R-Value Observed: 
  0.284 (Depositor) 

Starting Model: experimental

Literature

Domain Closure in Citrate Synthases Adapted to the Range of Biological Temperatures

Vogl, C., Hough, D.W., Danson, M.J., Crennell, S.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 166.54 kDa 
• Atom Count: 11,672 
• Modeled Residue Count: 1,452 
• Deposited Residue Count: 1,452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CITRATE SYNTHASE 1	A, B, C, D	363	Bacillus subtilis	Mutation(s): 0  EC: 2.3.3.1 (PDB Primary Data), 2.3.3.16 (UniProt)
UniProt
Find proteins for P39119 (Bacillus subtilis (strain 168)) Explore P39119  Go to UniProtKB:  P39119

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COZ	E [auth A], G [auth B], I [auth C], K [auth D]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-HDCXRZRFSA-N
CIT	F [auth A], H [auth B], J [auth C], L [auth D]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.316 (Depositor), 0.299 (DCC) 
• R-Value Work:  0.284 (Depositor), 0.269 (DCC) 
• R-Value Observed: 0.284 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.504	α = 90
b = 185.563	β = 106.62
c = 82.563	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-26 
Deposition Author(s): Vogl, C., Hough, D.W., Danson, M.J., Crennell, S.J.

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2025-10-01
  Changes: Advisory, Derived calculations, Structure summary