1VP2 | pdb_00001vp2

CRYSTAL STRUCTURE OF A PUTATIVE XANTHOSINE TRIPHOSPHATE PYROPHOSPHATASE/HAM1 PROTEIN HOMOLOG (TM0159) FROM THERMOTOGA MARITIMA AT 1.78 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1VP2/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-10-06 Released: 2004-10-26 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.205 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Putative Xanthosine triphosphate pyrophosphatase1/HAM1 protein homolog (TM0159) from Thermotoga maritima at 1.78 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.05 kDa 
• Atom Count: 3,247 
• Modeled Residue Count: 378 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Xanthosine triphosphate pyrophosphatase/HAM1 protein homolog	A, B	208	Thermotoga maritima	Mutation(s): 0  Gene Names: TM0159 EC: 3.6.1 (PDB Primary Data), 3.6.1.66 (UniProt)
UniProt
Find proteins for Q9WY06 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WY06  Go to UniProtKB:  Q9WY06

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.205 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VP2

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.851	α = 90
b = 142.851	β = 90
c = 45.082	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-26 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-20
  Changes: Data collection, Refinement description