1VMJ | pdb_00001vmj

CRYSTAL STRUCTURE OF A PUTATIVE THIAMIN PHOSPHATE SYNTHASE (TM0723) FROM THERMOTOGA MARITIMA MSB8 AT 1.52 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1VMJ/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: 1.52 Å
• R-Value Free: 
  0.163 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of hypothetical protein (TM0723) from Thermotoga maritima at 1.52 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,PQS (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.13 kDa 
• Atom Count: 1,398 
• Modeled Residue Count: 139 
• Deposited Residue Count: 151 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TM0723	A	151	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM0723
UniProt
Find proteins for Q9WZI2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZI2  Go to UniProtKB:  Q9WZI2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.163 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VMJ

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.194	α = 90
b = 110.194	β = 90
c = 110.194	γ = 90

Software Package:

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

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, Derived calculations, 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