3K96

2.1 Angstrom resolution crystal structure of glycerol-3-phosphate dehydrogenase (gpsA) from Coxiella burnetii

• PDB DOI: https://doi.org/10.2210/pdb3K96/pdb

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


• Deposited: 2009-10-15 Released: 2009-10-27 
• Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

2.1 Angstrom Resolution Crystal Structure of Glycerol-3-phosphate Dehydrogenase (gpsA) from Coxiella burnetii.

Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 78.27 kDa 
• Atom Count: 5,715 
• Modelled Residue Count: 651 
• Deposited Residue Count: 712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol-3-phosphate dehydrogenase [NAD(P)+]	A, B	356	Coxiella burnetii RSA 493	Mutation(s): 0  Gene Names: CBU_1518, gpsA EC: 1.1.1.94
UniProt
Find proteins for Q83BJ0 (Coxiella burnetii (strain RSA 493 / Nine Mile phase I)) Explore Q83BJ0  Go to UniProtKB:  Q83BJ0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth A], E [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
BME	D [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33k96

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.272	α = 90
b = 88.452	β = 90
c = 97.289	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description