7D1G | pdb_00007d1g

Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase GAPDH from Clostridium beijerinckii

• PDB DOI: https://doi.org/10.2210/pdb7D1G/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridium beijerinckii NCIMB 8052
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-09-14 Released: 2021-03-17 
• Deposition Author(s): Chen, Y., Lan, J., Liu, W., Wang, L., Xu, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.211 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase GAPDH from Clostridium beijerinckii

Chen, Y., Lan, J., Liu, W., Wang, L., Xu, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.03 kDa 
• Atom Count: 2,864 
• Modeled Residue Count: 333 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A	333	Clostridium beijerinckii NCIMB 8052	Mutation(s): 0  Gene Names: Cbei_0597 EC: 1.2.1
UniProt
Find proteins for A6LR04 (Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052)) Explore A6LR04  Go to UniProtKB:  A6LR04

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	B [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.211 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.64	α = 90
b = 120.64	β = 90
c = 122.135	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Chen, Y., Lan, J., Liu, W., Wang, L., Xu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31200556
National Natural Science Foundation of China (NSFC)	China	21272031

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Advisory, Data collection, Database references, Structure summary