3POR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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

Weiss, M.S.Schulz, G.E.

(1993) J.Mol.Biol. 231: 817-824

  • DOI: 10.1006/jmbi.1993.1328

  • 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 aci ...

    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.


    Related Citations: 
    • Molecular Architecture and Electrostatic Properties of a Bacterial Porin
      Weiss, M.S.,Abele, U.,Weckesser, J.,Welte, W.,Schiltz, E.,Schulz, G.E.
      (1991) Science 254: 1627
    • Primary Structure of Porin from Rhodobacter Capsulatus
      Schiltz, E.,Kreusch, A.,Nestel, U.,Schulz, G.E.
      (1991) Eur.J.Biochem. 199: 587
    • The Structure of Porin from Rhodobacter Capsulatus at 1.8 Angstroms Resolution
      Weiss, M.S.,Kreusch, A.,Schiltz, E.,Nestel, U.,Welte, W.,Weckesser, J.,Schulz, G.E.
      (1991) FEBS Lett. 280: 379
    • The Three-Dimensional Structure of Porin from Rhodobacter Capsulatus at 3 Angstroms Resolution
      Weiss, M.S.,Wacker, T.,Weckesser, J.,Welte, W.,Schulz, G.E.
      (1990) FEBS Lett. 267: 268
    • Structure of Porin Refined at 1.8 Angstroms Resolution
      Weiss, M.S.,Schulz, G.E.
      (1992) J.Mol.Biol. 227: 493
    • The Structure of Porin from Rhodobacter Capsulatus at 0.6 Nm Resolution
      Weiss, M.S.,Wacker, T.,Nestel, U.,Woitzik, D.,Weckesser, J.,Kreutz, W.,Welte, W.,Schulz, G.E.
      (1989) FEBS Lett. 256: 143
    • Crystallization and Preliminary X-Ray Analysis of Porin from Rhodobacter Capsulatus
      Nestel, U.,Wacker, T.,Woitzik, D.,Weckesser, J.,Kreutz, W.,Welte, W.
      (1989) FEBS Lett. 242: 405
    • Crystals of an Integral Membrane Protein Diffracting to 1.8 Angstroms Resolution
      Kreusch, A.,Weiss, M.S.,Welte, W.,Weckesser, J.,Schulz, G.E.
      (1991) J.Mol.Biol. 217: 9


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PORIN
A
301Rhodobacter capsulatusMutation(s): 0 
Find proteins for P31243 (Rhodobacter capsulatus)
Go to UniProtKB:  P31243
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E

Download SDF File 
Download CCD File 
A
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.188 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 95.300α = 90.00
b = 95.300β = 90.00
c = 146.800γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-07-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other