3POR | pdb_00003por

PORIN CONFORMATION IN THE ABSENCE OF CALCIUM; REFINED STRUCTURE AT 2.5 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3POR/pdb

• Classification: INTEGRAL MEMBRANE PROTEIN PORIN
• Organism(s): Rhodobacter capsulatus
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 1992-11-09 Released: 1993-07-15 
• Deposition Author(s): Weiss, M.S., Schulz, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.188 (Depositor), 0.178 (DCC) 

Literature

Porin conformation in the absence of calcium. Refined structure at 2.5 A resolution.

Weiss, M.S., Schulz, G.E.

(1993) J Mol Biology 231: 817-824

• PubMed: 7685826 
• DOI: https://doi.org/10.1006/jmbi.1993.1328
• Primary Citation Related Structures: 
  3POR


• PubMed Abstract: 
  

  The crystal structure of porin from Rhodobacter capsulatus in the absence of divalent calcium ions has been refined to convergence at a resolution of 2.5 A using the simulated annealing refinement method. The final model consists of all 301 amino acid residues, 77 solvent molecules, one tris(hydroxymethyl)-aminomethane molecule and one unknown ligand modeled as n-octyltetraoxyethylene. A superposition with the previously described model containing three calcium ions showed structural changes at the segment 108-116 of the inner loop beta 5-beta 6, and at loops beta 8-beta 9 and beta 11-beta 12 at the extracellular side of the porin molecule. Evidence is presented that the conformational changes depend on the presence or absence of calcium ions. A possible influence on porin function is discussed.

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Organizational Affiliation: 
• Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 31.98 kDa 
• Atom Count: 2,325 
• Modeled Residue Count: 301 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PORIN	A	301	Rhodobacter capsulatus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P31243 (Rhodobacter capsulatus) Explore P31243  Go to UniProtKB:  P31243

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8E	B [auth A]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.188 (Depositor), 0.178 (DCC) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.3	α = 90
b = 95.3	β = 90
c = 146.8	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-07-15 
Deposition Author(s): Weiss, M.S., Schulz, G.E.

Revision History  

• Version 1.0: 1993-07-15
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references, Derived calculations