3PQA | pdb_00003pqa

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase GapN from Methanocaldococcus jannaschii DSM 2661

• PDB DOI: https://doi.org/10.2210/pdb3PQA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-11-25 Released: 2010-12-15 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Seidel, R., Garrett, S., Foti, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase GapN from Methanocaldococcus jannaschii DSM 2661

Malashkevich, V.N., Toro, R., Seidel, R., Garrett, S., Foti, R., Almo, S.C.

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: 217.18 kDa 
• Atom Count: 15,744 
• Modeled Residue Count: 1,825 
• Deposited Residue Count: 1,944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactaldehyde dehydrogenase	A, B, C, D	486	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: MJ1411 EC: 1.2.1.22
UniProt
Find proteins for Q58806 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58806  Go to UniProtKB:  Q58806

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.574	α = 90
b = 77.568	β = 116.29
c = 164.279	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-15 
Deposition Author(s): Malashkevich, V.N., Toro, R., Seidel, R., Garrett, S., Foti, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2010-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description