5NHX | pdb_00005nhx

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 (Depositor), 0.193 (DCC)
R-Value Work:
0.176 (Depositor), 0.178 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 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
Modeled Residue Count: 126
Deposited Residue Count: 126
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.193 (DCC)
R-Value Work: 0.176 (Depositor), 0.178 (DCC)
R-Value Observed: 0.178 (Depositor)

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

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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
Version 1.2: 2024-11-13
Changes: 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.