3VAZ

Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group

• PDB DOI: https://doi.org/10.2210/pdb3VAZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus subsp. aureus MRSA252
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-30 Released: 2013-01-02 
• Deposition Author(s): Roychowdhury, A., Mukherjee, S., Dutta, D., Das, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.277 
• R-Value Work: 0.202 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group

Roychowdhury, A., Mukherjee, S., Dutta, D., Das, A.K.

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)

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 PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 228.53 kDa 
• Atom Count: 15,730 
• Modelled Residue Count: 2,005 
• Deposited Residue Count: 2,064 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase 1	A [auth P], B [auth R], C [auth O], D [auth Q], E [auth B], F [auth A]	344	Staphylococcus aureus subsp. aureus MRSA252	Mutation(s): 0  Gene Names: gap, gapA, gapA1, SAR0828 EC: 1.2.1.12
UniProt
Find proteins for Q6GIL8 (Staphylococcus aureus (strain MRSA252)) Explore Q6GIL8  Go to UniProtKB:  Q6GIL8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	G [auth P], K [auth R], L [auth O], O [auth Q], P [auth B], R [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
DGY	N [auth O], T [auth A]	(2R)-2,3-DIHYDROXYPROPANOIC ACID C3 H6 O4 RBNPOMFGQQGHHO-UWTATZPHSA-N
PO4	H [auth P], I [auth P], J [auth P], M [auth O], Q [auth B], S [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.277 
• R-Value Work: 0.202 
• R-Value Observed: 0.206 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.389	α = 90
b = 155.389	β = 90
c = 317.849	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-02 
Deposition Author(s): Roychowdhury, A., Mukherjee, S., Dutta, D., Das, A.K.

Revision History  

• Version 1.0: 2013-01-02
  Type: Initial release
  
• Version 1.1: 2014-11-12
  Changes: Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description