4HN7 | pdb_00004hn7

Crystal structure of E. coli PmrD

PDB DOI: https://doi.org/10.2210/pdb4HN7/pdb

Classification: SIGNALING PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-10-19 Released: 2013-10-23
Deposition Author(s): Jeong, E., Jung, H., Ban, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.281 (Depositor), 0.290 (DCC)
R-Value Work:
0.211 (Depositor), 0.220 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of E. coli PmrD

Jeong, E., Jung, H., Ban, C.

To be published.

Macromolecule Content

Total Structure Weight: 9.89 kDa
Atom Count: 668
Modeled Residue Count: 85
Deposited Residue Count: 88
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal transduction protein pmrD	A	88	Escherichia coli K-12	Mutation(s): 0 Gene Names: b2259, JW2254, pmrD
UniProt
Find proteins for P37590 (Escherichia coli (strain K12)) Explore P37590 Go to UniProtKB: P37590
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P37590
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.281 (Depositor), 0.290 (DCC)
R-Value Work: 0.211 (Depositor), 0.220 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.58	α = 90
b = 83.58	β = 90
c = 75.951	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-10-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-23
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary

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.