1WN1 | pdb_00001wn1

Crystal Structure of Dipeptiase from Pyrococcus Horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb1WN1/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-07-26 Released: 2005-08-09 
• Deposition Author(s): Jeyakanthan, J., Taka, J., Kitaguchi, Y., Shiro, Y., Yokoyama, S., Yutani, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.248 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal Structure of Dipeptiase from Pyrococcus Horikoshii OT3

Jeyakanthan, J., Taka, J., Kitaguchi, Y., Shiro, Y., Yokoyama, S., Yutani, K.

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 (software)

Macromolecule Content 

• Total Structure Weight: 80.7 kDa 
• Atom Count: 6,143 
• Modeled Residue Count: 712 
• Deposited Residue Count: 712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dipeptidase	A, B	356	Pyrococcus horikoshii OT3	Mutation(s): 0  EC: 3.4
UniProt
Find proteins for O58691 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58691  Go to UniProtKB:  O58691

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	C [auth A], D [auth A], E [auth B], F [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.248 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.966	α = 90
b = 89.002	β = 90
c = 147.159	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-09 
Deposition Author(s): Jeyakanthan, J., Taka, J., Kitaguchi, Y., Shiro, Y., Yokoyama, S., Yutani, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-08-09
  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: 2024-03-13
  Changes: Data collection, Database references, Derived calculations