1VBK | pdb_00001vbk

Crystal structure of PH1313 from Pyrococcus horikoshii Ot3

• PDB DOI: https://doi.org/10.2210/pdb1VBK/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-02-27 Released: 2005-04-19 
• Deposition Author(s): Sugahara, M., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.222 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Purification, crystallization and preliminary crystallographic analysis of the putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3

Sugahara, M., Murai, S., Sugahara, M., Kunishima, N.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 56-58

• PubMed: 17183176 
• DOI: https://doi.org/10.1107/S1744309106054509
• Primary Citation Related Structures: 
  1VBK


• PubMed Abstract: 
  

  The putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3 has been overexpressed and purified. Crystallization was performed by the oil-microbatch method using 28%(v/v) 2-methyl-2,4-pentanediol as a precipitant at 291 K. A native X-ray diffraction data set at 1.9 A resolution and a single anomalous dispersion data set from a selenomethionine-derivative crystal at 2.1 A resolution were collected using synchrotron radiation at 100 K. The native crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 71.7, b = 71.2, c = 141.8 A.

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Organizational Affiliation: 
• Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.

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: 70.88 kDa 
• Atom Count: 5,540 
• Modeled Residue Count: 603 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein PH1313	A, B	307	Pyrococcus horikoshii OT3	Mutation(s): 0
UniProt
Find proteins for O59053 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59053  Go to UniProtKB:  O59053

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	C [auth A], D [auth A], E [auth B], F [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.222 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.743	α = 90
b = 71.164	β = 90
c = 141.774	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: 2005-04-19 
Deposition Author(s): Sugahara, M., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations