3UPG | pdb_00003upg

Loop deletion mutant of Salmonella typhi osmoporin (OmpC):an Outer Membrane Protein.

• PDB DOI: https://doi.org/10.2210/pdb3UPG/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2011-11-18 Released: 2012-11-28 
• Deposition Author(s): Prasanth, P., Putcha, B.K., Arockiasamy, A., Krishnaswamy, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.325 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.288 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.290 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of osmoporin (OmpC) loop deletion mutant: an Outer membrane protein from Salmonella typhi.

Prasanth, P., Putcha, B.K., Arockiasamy, A., Krishnaswamy, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 37.48 kDa 
• Atom Count: 2,449 
• Modeled Residue Count: 311 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein C	A	338	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: ompC, STM2267 Membrane Entity: Yes
UniProt
Find proteins for P0A264 (Salmonella typhi) Explore P0A264  Go to UniProtKB:  P0A264

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.325 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.288 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.290 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.149	α = 90
b = 115.149	β = 90
c = 216.736	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-28 
Deposition Author(s): Prasanth, P., Putcha, B.K., Arockiasamy, A., Krishnaswamy, S.

Revision History  

• Version 1.0: 2012-11-28
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description