1VMK | pdb_00001vmk

Crystal structure of Purine nucleoside phosphorylase (TM1596) from Thermotoga maritima at 2.01 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VMK/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-09-30 Released: 2004-10-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.240 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Purine nucleoside phosphorylase (TM1596) from Thermotoga maritima at 2.01 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 92.5 kDa 
• Atom Count: 5,969 
• Modeled Residue Count: 740 
• Deposited Residue Count: 831 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
purine nucleoside phosphorylase	A, B, C	277	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM1596 EC: 2.4.2.1
UniProt
Find proteins for Q9X1T2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1T2  Go to UniProtKB:  Q9X1T2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GUN	D [auth A], F [auth B], G [auth C]	GUANINE C5 H5 N5 O UYTPUPDQBNUYGX-UHFFFAOYSA-N
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.240 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VMK

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.478	α = 117.34
b = 74.601	β = 100.95
c = 74.591	γ = 100.71

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-10-12
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, 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