2HTM | pdb_00002htm

Crystal structure of TTHA0676 from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2HTM/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-07-26 Released: 2007-01-26 
• 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: 2.30 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of TTHA0676 from Thermus thermophilus HB8

Sugahara, M., Kunishima, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 142.46 kDa 
• Atom Count: 9,392 
• Modeled Residue Count: 1,198 
• Deposited Residue Count: 1,328 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiazole biosynthesis protein thiG	A, B, C, D	268	Thermus thermophilus	Mutation(s): 0  EC: 2.8.1.10
UniProt
Find proteins for Q5SKG7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKG7  Go to UniProtKB:  Q5SKG7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative thiamine biosynthesis protein ThiS	E, F, G, H	64	Thermus thermophilus	Mutation(s): 3
UniProt
Find proteins for Q5SKG8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKG8  Go to UniProtKB:  Q5SKG8

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.339	α = 68.64
b = 73.511	β = 80.16
c = 100.911	γ = 79.09

Software Package:

Software Name	Purpose
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-26 
Deposition Author(s): Sugahara, M., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-01-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary