2DCT | pdb_00002dct

Crystal structure of the TT1209 from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2DCT/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-12 Released: 2006-01-24 
• Deposition Author(s): Asada, Y., Sugahara, M., Shimizu, K., Yamamoto, H., Shimada, H., Nakamoto, T., Ono, N., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.209 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the TT1209 from Thermus thermophilus HB8

Asada, Y., Sugahara, M., Shimizu, K., Yamamoto, H., Shimada, H., Misumi, Y., Nakamoto, T., Ono, N., Kunishima, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.06 kDa 
• Atom Count: 2,000 
• Modeled Residue Count: 210 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TTHA0104	A, B	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SM39 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SM39  Go to UniProtKB:  Q5SM39

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.209 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.241	α = 90
b = 62.241	β = 90
c = 151.11	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
PERON	model building
CNS	refinement
HKL-2000	data reduction
PERON	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-24 
Deposition Author(s): Asada, Y., Sugahara, M., Shimizu, K., Yamamoto, H., Shimada, H., Nakamoto, T., Ono, N., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-01-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description