3GVX | pdb_00003gvx

Crystal structure of Glycerate dehydrogenase related protein from Thermoplasma acidophilum

• PDB DOI: https://doi.org/10.2210/pdb3GVX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermoplasma acidophilum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-31 Released: 2009-04-28 
• Deposition Author(s): Syed Ibrahim, B., Kumaran, D., 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: 2.20 Å
• R-Value Free: 
  0.261 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

Crystal Structure of Glycerate dehydrogenase related protein from Thermoplasma acidophilum

Syed Ibrahim, B., Kumaran, D., Burley, S.K., Swaminathan, S.

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: 65.28 kDa 
• Atom Count: 4,676 
• Modeled Residue Count: 571 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerate dehydrogenase related protein	A, B	290	Thermoplasma acidophilum	Mutation(s): 0  Gene Names: Ta0858 EC: 1.1.1.2
UniProt
Find proteins for Q9HJV5 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HJV5  Go to UniProtKB:  Q9HJV5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	C [auth A], D [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.261 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.512	α = 90
b = 77.842	β = 90
c = 152.654	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-28 
Deposition Author(s): Syed Ibrahim, B., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary