4DIB | pdb_00004dib

The crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Bacillus anthracis str. Sterne

• PDB DOI: https://doi.org/10.2210/pdb4DIB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus anthracis str. Sterne
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-30 Released: 2012-02-22 
• Deposition Author(s): Nocek, B., Makowska-Grzyska, M., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.270 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Bacillus anthracis str. Sterne

Nocek, B., Makowska-Grzyska, M., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 303.31 kDa 
• Atom Count: 19,464 
• Modeled Residue Count: 2,555 
• Deposited Residue Count: 2,760 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde 3-phosphate dehydrogenase	A, B, C, D, E, F, G, H	345	Bacillus anthracis str. Sterne	Mutation(s): 0  Gene Names: gap1, BA_4827, BAS4478, GBAA_4827 EC: 1.2.1.12 (PDB Primary Data), 1.2.1 (UniProt)
UniProt
Find proteins for A0A348AAL1 (Bacillus anthracis) Explore A0A348AAL1  Go to UniProtKB:  A0A348AAL1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth C], K [auth D], L [auth E], M [auth F], N [auth H], O [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.270 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34dib

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.347	α = 90.32
b = 102.044	β = 73.99
c = 102.144	γ = 68.99

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-22 
Deposition Author(s): Nocek, B., Makowska-Grzyska, M., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Advisory, Database references
• Version 1.2: 2023-09-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description