2D5W

The crystal structure of oligopeptide binding protein from Thermus thermophilus HB8 complexed with pentapeptide

• PDB DOI:  https://doi.org/10.2210/pdb2D5W/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-11-07 Released: 2006-10-17 
• Deposition Author(s): Morita, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.196 
• R-Value Work: 0.186 

Literature

The crystal structure of oligopeptide binding protein from Thermus thermophilus HB8 complexed with pentapeptide

Morita, A., Sakai, N., Yao, M., Watanabe, N., Tanaka, I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 138.48 kDa 
• Atom Count: 10,842 
• Modelled Residue Count: 1,214 
• Deposited Residue Count: 1,216 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide ABC transporter, peptide-binding protein	A, B	603	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA1634
UniProt
Find proteins for Q5SHU6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHU6  Go to UniProtKB:  Q5SHU6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
pentapeptide A	C	5	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA1634

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
pentapeptide B	D	5	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA1634

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.196 
• R-Value Work: 0.186 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.6	α = 90
b = 109.2	β = 90
c = 114.6	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
TRUNCATE	data reduction
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Morita, A.

Revision History  

• Version 1.0: 2006-10-17
  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