3RHH | pdb_00003rhh

Crystal structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Bacillus halodurans C-125 complexed with NADP

• PDB DOI: https://doi.org/10.2210/pdb3RHH/pdb

• Classification: TRANSFERASE
• Organism(s): Halalkalibacterium halodurans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-11 Released: 2011-05-18 
• 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: 2.30 Å
• R-Value Free: 
  0.297 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Bacillus halodurans C-125 complexed with NADP

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: 221.62 kDa 
• Atom Count: 14,718 
• Modeled Residue Count: 1,907 
• Deposited Residue Count: 2,020 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D	505	Halalkalibacterium halodurans	Mutation(s): 0  Gene Names: BAB05956.1, BH2237, gapN EC: 1.2.1.9
UniProt
Find proteins for Q9KAQ0 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KAQ0  Go to UniProtKB:  Q9KAQ0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], G [auth B], I [auth C], K [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
SO4	F [auth A], H [auth B], J [auth C], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.297 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.649	α = 90
b = 130.753	β = 102.69
c = 86.918	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: 2011-05-18 
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: 2011-05-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description