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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (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

Entry History 

Deposition Data

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

Revision History  

• 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