1V9N | pdb_00001v9n

Structure of Malate Dehydrogenase from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb1V9N/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-01-26 Released: 2005-03-29 
• Deposition Author(s): Lokanath, N.K., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.243 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Structure of Malate Dehydrogenase from Pyrococcus horikoshii OT3

Lokanath, N.K., Kunishima, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 41.16 kDa 
• Atom Count: 2,863 
• Modeled Residue Count: 348 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A	360	Pyrococcus horikoshii OT3	Mutation(s): 11  EC: 1.1.1.37
UniProt
Find proteins for O59028 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59028  Go to UniProtKB:  O59028

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.10 Å
• R-Value Free:  0.243 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.19	α = 90
b = 74.19	β = 90
c = 127.28	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-29 
Deposition Author(s): Lokanath, N.K., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-03-29
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Structure summary