4BOY | pdb_00004boy

Structure of GAPDH from Thermosynechococcus elongatus

• PDB DOI: https://doi.org/10.2210/pdb4BOY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermosynechococcus vestitus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-22 Released: 2014-06-11 
• Deposition Author(s): Cotton, C.A.R., Murray, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.201 (Depositor) 
• R-Value Work: 
  0.166 (Depositor) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Structure of Gapdh

Cotton, C.A.R., Murray, J.W.

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)

Macromolecule Content 

• Total Structure Weight: 78.48 kDa 
• Atom Count: 5,407 
• Modeled Residue Count: 676 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE	A, B	354	Thermosynechococcus vestitus	Mutation(s): 0  EC: 1.2.1.13 (PDB Primary Data), 1.2.1 (UniProt)
UniProt
Find proteins for Q8DIW5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIW5  Go to UniProtKB:  Q8DIW5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.201 (Depositor) 
• R-Value Work:  0.166 (Depositor) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.92	α = 90
b = 141.92	β = 90
c = 76.06	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-11 
Deposition Author(s): Cotton, C.A.R., Murray, J.W.

Revision History  

• Version 1.0: 2014-06-11
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description