4EZU | pdb_00004ezu

Crystal structure of the substrate binding domain of E.coli DnaK in complex with PR-bombesin in space group I222

PDB DOI: https://doi.org/10.2210/pdb4EZU/pdb

Classification: CHAPERONE/PEPTIDE BINDING PROTEIN
Organism(s): Escherichia coli K-12, Bombina maxima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-05-03 Released: 2013-04-24
Deposition Author(s): Zahn, M., Straeter, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.276 (Depositor), 0.275 (DCC)
R-Value Work:
0.218 (Depositor), 0.217 (DCC)
R-Value Observed:
0.221 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4EZU

This is version 1.2 of the entry. See complete history.

Literature

Structural studies of DnaK in complex with proline rich antimicrobial peptides reveal two different peptide binding modes

Zahn, M., Straeter, N.

To be published.

Macromolecule Content

Total Structure Weight: 25.86 kDa
Atom Count: 1,849
Modeled Residue Count: 230
Deposited Residue Count: 236
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein DnaK	A	219	Escherichia coli K-12	Mutation(s): 0 Gene Names: b0014, dnaK, groP, grpF, JW0013, seg
UniProt
Find proteins for P0A6Y8 (Escherichia coli (strain K12)) Explore P0A6Y8 Go to UniProtKB: P0A6Y8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6Y8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline rich bombesin-related protein	B	17	Bombina maxima	Mutation(s): 0
UniProt
Find proteins for Q8QFP2 (Bombina maxima) Explore Q8QFP2 Go to UniProtKB: Q8QFP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8QFP2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.276 (Depositor), 0.275 (DCC)
R-Value Work: 0.218 (Depositor), 0.217 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.645	α = 90
b = 115.047	β = 90
c = 39.366	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-04-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-24
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.