7D1G

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.211
R-Value Work: 0.193
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6LR04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.193
R-Value Observed: 0.194
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-03-17

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2021-03-17
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.