1WNF | pdb_00001wnf

Crystal Structure of PH0066 from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb1WNF/pdb

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


• Deposited: 2004-08-02 Released: 2005-02-02 
• Deposition Author(s): Ihsanawati, Sekine, S., Murayama, K., Sugawara, M., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of PH0066 from Pyrococcus horikoshii

Ihsanawati, Sekine, S., Murayama, K., Sugawara, M., Shirouzu, M., Yokoyama, S.

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: 72.87 kDa 
• Atom Count: 5,437 
• Modeled Residue Count: 648 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase	A, B	328	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH0066 EC: 3.5.1.1
UniProt
Find proteins for O57797 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57797  Go to UniProtKB:  O57797

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.23	α = 90
b = 77.14	β = 90
c = 98.46	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-02 
Deposition Author(s): Ihsanawati, Sekine, S., Murayama, K., Sugawara, M., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-02-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description