1VDW | pdb_00001vdw

A hypothetical protein PH1897 from Pyrococcus horikoshii with similarities for Inositol-1 monophosphatase

• PDB DOI: https://doi.org/10.2210/pdb1VDW/pdb

• Classification: structural genomics, unknown function
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-03-25 Released: 2004-04-06 
• Deposition Author(s): Inagaki, E., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.217 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of hypothetical protein PH1897 from Pyrococcus horikoshii with similarities for Inositol-1-monophosphatase.

Inagaki, E., Tahirov, T.H.

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.

Macromolecule Content

• Total Structure Weight: 56.54 kDa 
• Atom Count: 4,818 
• Modelled Residue Count: 496 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein PH1897	A, B	254	Pyrococcus horikoshii	Mutation(s): 0  EC: 3.1.3.11
UniProt
Find proteins for O59523 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59523  Go to UniProtKB:  O59523

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.217 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.989	α = 90
b = 89.762	β = 90
c = 120.576	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-06 
Deposition Author(s): Inagaki, E., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2004-04-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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