4ERH | pdb_00004erh

The crystal structure of OmpA domain of OmpA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

• PDB DOI: https://doi.org/10.2210/pdb4ERH/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-20 Released: 2012-05-02 
• Deposition Author(s): Tan, K., Wu, R., Jedrzejczak, R., Adkins, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Program for the Characterization of Secreted Effector Proteins (PCSEP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 
  0.268 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

The crystal structure of OmpA domain of OmpA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Tan, K., Wu, R., Jedrzejczak, R., Adkins, J., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.49 kDa 
• Atom Count: 2,051 
• Modeled Residue Count: 257 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein A	A, B	148	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S	Mutation(s): 0  Gene Names: ompA, STM14_1214
UniProt
Find proteins for A0A0F6AZN3 (Salmonella typhimurium (strain 14028s / SGSC 2262)) Explore A0A0F6AZN3  Go to UniProtKB:  A0A0F6AZN3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], F [auth B], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free:  0.268 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.435	α = 90
b = 109.435	β = 90
c = 56.392	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Tan, K., Wu, R., Jedrzejczak, R., Adkins, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Program for the Characterization of Secreted Effector Proteins (PCSEP)

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Structure summary
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary