2DJW

Crystal structure of TTHA0845 from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2DJW/pdb

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


• Deposited: 2006-04-05 Released: 2006-09-12 
• Deposition Author(s): Okazaki, N., Nakano, N., Shinkai, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.294 
• R-Value Work: 0.250 
• R-Value Observed: 0.252 

Literature

Structure of the stand-alone RAM-domain protein from Thermus thermophilus HB8

Nakano, N., Okazaki, N., Satoh, S., Takio, K., Kuramitsu, S., Shinkai, A., Yokoyama, S.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 855-860

• PubMed: 16946463 
• DOI: https://doi.org/10.1107/S1744309106031150
• Primary Citation of Related Structures:  
  2DJW


• PubMed Abstract: 
  

  The stand-alone RAM (regulation of amino-acid metabolism) domain protein SraA from Thermus thermophilus HB8 (TTHA0845) was crystallized in the presence of zinc ions. The X-ray crystal structure was determined using a multiple-wavelength anomalous dispersion technique and was refined at 2.4 A resolution to a final R factor of 25.0%. The monomeric structure is a betaalphabetabetaalphabeta fold and it dimerizes mainly through interactions between the antiparallel beta-sheets. Furthermore, five SraA dimers form a ring with external and internal diameters of 70 and 20 A, respectively. This decameric structure is unique compared with the octameric and dodecameric structures found for other stand-alone RAM-domain proteins and the C-terminal RAM domains of Lrp/AsnC-family proteins.

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Organizational Affiliation: 

RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Macromolecule Content

• Total Structure Weight: 101.48 kDa 
• Atom Count: 6,447 
• Modelled Residue Count: 799 
• Deposited Residue Count: 920 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
probable transcriptional regulator, AsnC family	A, B, C, D, E, F, G, H, I, J	92	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SK07 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SK07  Go to UniProtKB:  Q5SK07

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	K [auth B], L [auth E], M [auth G], N [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.294 
• R-Value Work: 0.250 
• R-Value Observed: 0.252 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.883	α = 90
b = 95.883	β = 90
c = 119.01	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-12 
Deposition Author(s): Okazaki, N., Nakano, N., Shinkai, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-09-12
  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: 2024-03-13
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description