2DST | pdb_00002dst

Crystal Structure Analysis of TT1977

• PDB DOI: https://doi.org/10.2210/pdb2DST/pdb

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


• Deposited: 2006-07-06 Released: 2007-01-06 
• Deposition Author(s): Xie, Y., Kishishita, S., Murayama, K., Shirouzu, M., Chen, L., Liu, Z.J., Wang, B.C., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.245 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Structure of the minimized alpha/beta-hydrolase fold protein from Thermus thermophilus HB8.

Xie, Y., Takemoto, C., Kishishita, S., Uchikubo-Kamo, T., Murayama, K., Chen, L., Liu, Z.J., Wang, B.C., Manzoku, M., Ebihara, A., Kuramitsu, S., Shirouzu, M., Yokoyama, S.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 993-997

• PubMed: 18084077 
• DOI: https://doi.org/10.1107/S1744309107061106
• Primary Citation Related Structures: 
  2DST


• PubMed Abstract: 
  

  The gene encoding TTHA1544 is a singleton found in the Thermus thermophilus HB8 genome and encodes a 131-amino-acid protein. The crystal structure of TTHA1544 has been determined at 2.0 A resolution by the single-wavelength anomalous dispersion method in order to elucidate its function. There are two molecules in the asymmetric unit. Each molecule consists of four alpha-helices and six beta-strands, with the beta-strands composing a central beta-sheet. A structural homology search revealed that the overall structure of TTHA1544 resembles the alpha/beta-hydrolase fold, although TTHA1544 lacks the catalytic residues of a hydrolase. These results suggest that TTHA1544 represents the minimized alpha/beta-hydrolase fold and that an additional component would be required for its activity.

---

Organizational Affiliation: 
• Protein Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.16 kDa 
• Atom Count: 2,004 
• Modeled Residue Count: 244 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein TTHA1544	A, B	131	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SI36 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SI36  Go to UniProtKB:  Q5SI36

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.245 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.714	α = 90
b = 65.822	β = 92.61
c = 59.32	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-06 
Deposition Author(s): Xie, Y., Kishishita, S., Murayama, K., Shirouzu, M., Chen, L., Liu, Z.J., Wang, B.C., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-01-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references