2PE3 | pdb_00002pe3

Crystal structure of Frv operon protein FRVX (PH1821)from pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb2PE3/pdb

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


• Deposited: 2007-04-02 Released: 2007-10-02 
• Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Rafi, Z.A., Sekar, K., Inagakai, E., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.197 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of frv operon protein frvx (ph1821)from pyrococcus horikoshii OT3

Jeyakanthan, J., Kanaujia, S.P., Rafi, Z.A., Sekar, K., Inagaki, E., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 156.24 kDa 
• Atom Count: 10,804 
• Modeled Residue Count: 1,318 
• Deposited Residue Count: 1,416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
354aa long hypothetical operon protein Frv	A, B, C, D	354	Pyrococcus horikoshii OT3	Mutation(s): 0
UniProt
Find proteins for O59485 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59485  Go to UniProtKB:  O59485

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.197 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.608	α = 90
b = 125.608	β = 90
c = 277.323	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Rafi, Z.A., Sekar, K., Inagakai, E., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Refinement description