4OFX | pdb_00004ofx

Crystal Structure of a Putative Cystathionine beta-Synthase from Coxiella burnetii

• PDB DOI: https://doi.org/10.2210/pdb4OFX/pdb

• Classification: LYASE
• Organism(s): Coxiella burnetii RSA 493
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-15 Released: 2014-02-05 
• Deposition Author(s): Brunzelle, J.S., Wawrzak, Z., Onopriyenko, O., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Putative Cystathionine beta-Synthase from Coxiella burnetii

Brunzelle, J.S., Wawrzak, Z., Onopriyenko, O., Savchenko, A., Anderson, W.F.

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 PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.67 kDa 
• Atom Count: 2,471 
• Modeled Residue Count: 288 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine beta-synthase	A	319	Coxiella burnetii RSA 493	Mutation(s): 0  Gene Names: CBU_2024 EC: 4.2.1.22 (PDB Primary Data), 2.5.1.47 (UniProt)
UniProt
Find proteins for Q83A84 (Coxiella burnetii (strain RSA 493 / Nine Mile phase I)) Explore Q83A84  Go to UniProtKB:  Q83A84

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34ofx

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.171	α = 90
b = 99.739	β = 90
c = 42.497	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
MrBump/MolRep	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-05 
Deposition Author(s): Brunzelle, J.S., Wawrzak, Z., Onopriyenko, O., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-02-05
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description