2DEH | pdb_00002deh

Crystal structure of tt0972 protein form Thermus Thermophilus with Cl(-) ions

• PDB DOI: https://doi.org/10.2210/pdb2DEH/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-02-10 Released: 2007-05-01 
• Deposition Author(s): Inagaki, E., Nakano, N., Shinkai, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.279 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: other

Literature

Crystal structure of tt0972 protein form Thermus Thermophilus

Inagaki, E., Nakano, N., Shinkai, A., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 46.65 kDa 
• Atom Count: 3,267 
• Modeled Residue Count: 404 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tt0972 protein	A, B, C, D, E, F	69	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q72IR6 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72IR6  Go to UniProtKB:  Q72IR6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	H [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.279 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.171	α = 90
b = 65.171	β = 90
c = 202.364	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: 2007-05-01 
Deposition Author(s): Inagaki, E., Nakano, N., Shinkai, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2026-03-04
  Changes: Refinement description, Structure summary