3GNQ

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from Burkholderia pseudomallei

PDB DOI: https://doi.org/10.2210/pdb3GNQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia pseudomallei 1710b
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-17 Released: 2009-03-24
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.263
R-Value Work: 0.204
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from Burkholderia pseudomallei

Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 302.2 kDa
Atom Count: 21,007
Modelled Residue Count: 2,679
Deposited Residue Count: 2,752
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, type I	A, B, C, D, E A, B, C, D, E, F, G, H	344	Burkholderia pseudomallei 1710b	Mutation(s): 0 Gene Names: gap, BURPS1710b_3466 EC: 1.2.1
UniProt
Find proteins for Q3JNL6 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JNL6 Go to UniProtKB: Q3JNL6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3JNL6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth E] SDF format, chain M [auth F] SDF format, chain N [auth G] SDF format, chain O [auth H] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth E] MOL2 format, chain M [auth F] MOL2 format, chain N [auth G] MOL2 format, chain O [auth H] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth E] mmCIF format, chain M [auth F] mmCIF format, chain N [auth G] mmCIF format, chain O [auth H]	I [auth B] J [auth C] K [auth D] L [auth E] M [auth F] I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F] Focus chain N [auth G] Focus chain O [auth H] Interactions & Density Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F] Focus chain N [auth G] Focus chain O [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.263
R-Value Work: 0.204
R-Value Observed: 0.207
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.932	α = 90
b = 173.797	β = 93.29
c = 93.501	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
COMO	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-03-24

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2009-03-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

Prepare Data

Validate Data

Deposit Data

Help and Resources

3GNQ

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from Burkholderia pseudomallei

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from Burkholderia pseudomallei

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)