5NHX

Periplasmic domain of Outer Membrane Protein A from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb5NHX/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-22 Released: 2018-05-16
Deposition Author(s): Demange, P., Tranier, S., Nars, G., Iordanov, I., Mourey, L., Saurel, O., Milon, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.194
R-Value Work: 0.176
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure and dynamics of the C-terminal domain of OmpA from Klebsiella pneumonia

Nars, G., Iordanov, I., Saurel, O., Tranier, S., Mourey, L., Milon, A., Demange, P.

To be published.

Macromolecule Content

Total Structure Weight: 13.84 kDa
Atom Count: 1,141
Modelled Residue Count: 126
Deposited Residue Count: 126
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein A	A	126	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: ompA
UniProt
Find proteins for P24017 (Klebsiella pneumoniae) Explore P24017 Go to UniProtKB: P24017
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24017
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.194
R-Value Work: 0.176
R-Value Observed: 0.178
Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.65	α = 90
b = 73.65	β = 90
c = 61.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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 R01GM133198.