2D8A | pdb_00002d8a

Crystal Structure of PH0655 from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb2D8A/pdb

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


• Deposited: 2005-12-02 Released: 2006-06-02 
• Deposition Author(s): Asada, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.235 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal Structure of PH0655 from Pyrococcus horikoshii OT3

Asada, Y., Kunishima, N.

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.

Macromolecule Content 

• Total Structure Weight: 39.14 kDa 
• Atom Count: 2,852 
• Modeled Residue Count: 333 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable L-threonine 3-dehydrogenase	A	348	Pyrococcus horikoshii OT3	Mutation(s): 7  EC: 1.1.1.103
UniProt
Find proteins for O58389 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58389  Go to UniProtKB:  O58389

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	G [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-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: 2.05 Å
• R-Value Free:  0.235 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.084	α = 90
b = 89.436	β = 90
c = 122.413	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-02 
Deposition Author(s): Asada, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-06-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary