2D5W | pdb_00002d5w

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.196 (Depositor)
R-Value Work:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHU6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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

Find similar proteins by: Sequence | 3D Structure

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 (Depositor)
R-Value Work: 0.186 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2006-10-17

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.