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Yorodumi- PDB-3por: PORIN CONFORMATION IN THE ABSENCE OF CALCIUM; REFINED STRUCTURE A... -
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-Basic information
Entry | Database: PDB / ID: 3por | ||||||
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Title | PORIN CONFORMATION IN THE ABSENCE OF CALCIUM; REFINED STRUCTURE AT 2.5 ANGSTROMS RESOLUTION | ||||||
Components | PORIN | ||||||
Keywords | INTEGRAL MEMBRANE PROTEIN PORIN | ||||||
Function / homology | Function and homology information porin activity / pore complex / monoatomic ion transport / cell outer membrane Similarity search - Function | ||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Weiss, M.S. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Porin conformation in the absence of calcium. Refined structure at 2.5 A resolution. Authors: Weiss, M.S. / Schulz, G.E. #1: Journal: J.Mol.Biol. / Year: 1992 Title: Structure of Porin Refined at 1.8 Angstroms Resolution Authors: Weiss, M.S. / Schulz, G.E. #2: Journal: Science / Year: 1991 Title: Molecular Architecture and Electrostatic Properties of a Bacterial Porin Authors: Weiss, M.S. / Abele, U. / Weckesser, J. / Welte, W. / Schiltz, E. / Schulz, G.E. #3: Journal: Eur.J.Biochem. / Year: 1991 Title: Primary Structure of Porin from Rhodobacter Capsulatus Authors: Schiltz, E. / Kreusch, A. / Nestel, U. / Schulz, G.E. #4: Journal: FEBS Lett. / Year: 1991 Title: The Structure of Porin from Rhodobacter Capsulatus at 1.8 Angstroms Resolution Authors: Weiss, M.S. / Kreusch, A. / Schiltz, E. / Nestel, U. / Welte, W. / Weckesser, J. / Schulz, G.E. #5: Journal: J.Mol.Biol. / Year: 1991 Title: Crystals of an Integral Membrane Protein Diffracting to 1.8 Angstroms Resolution Authors: Kreusch, A. / Weiss, M.S. / Welte, W. / Weckesser, J. / Schulz, G.E. #6: Journal: FEBS Lett. / Year: 1990 Title: The Three-Dimensional Structure of Porin from Rhodobacter Capsulatus at 3 Angstroms Resolution Authors: Weiss, M.S. / Wacker, T. / Weckesser, J. / Welte, W. / Schulz, G.E. #7: Journal: FEBS Lett. / Year: 1989 Title: The Structure of Porin from Rhodobacter Capsulatus at 0.6 Nm Resolution Authors: Weiss, M.S. / Wacker, T. / Nestel, U. / Woitzik, D. / Weckesser, J. / Kreutz, W. / Welte, W. / Schulz, G.E. #8: Journal: FEBS Lett. / Year: 1989 Title: Crystallization and Preliminary X-Ray Analysis of Porin from Rhodobacter Capsulatus Authors: Nestel, U. / Wacker, T. / Woitzik, D. / Weckesser, J. / Kreutz, W. / Welte, W. | ||||||
History |
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Remark 700 | SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A SIXTEEN-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A SIXTEEN-STRANDED BETA-BARREL. THIS IS REPRESENTED AS A SEVENTEEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3por.cif.gz | 70.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3por.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 3por.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/3por ftp://data.pdbj.org/pub/pdb/validation_reports/po/3por | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUE 117 IS A CIS PROLINE. 2: RESIDUE 545 HAS NOT BEEN UNAMBIGUOUSLY IDENTIFIED. IT HAS BEEN MODELED AS A DETERGENT N-OCTYLTETRAOXYETHYLENE. 3: FOURTEEN DETERGENT FRAGMENTS HAVE BEEN MODELED AS WATERS (SEE REMARK 5) | |||||||||
Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31555.424 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / References: UniProt: P31243 |
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#2: Chemical | ChemComp-C8E / ( |
#3: Chemical | ChemComp-TRS / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | FOURTEEN DETERGENT FRAGMENTS HAVE BEEN MODELED AS WATERS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.74 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 9999 Å / Num. all: 69237 / Num. obs: 16568 / % possible obs: 95.1 % / Rmerge(I) obs: 0.052 |
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-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.5→10 Å / Rfactor Rwork: 0.188 Details: THE AUTHORS REFER TO THIS STRUCTURE AS CRYSTAL FORM-A'. RESIDUE 545 HAS NOT BEEN UNAMBIGUOUSLY IDENTIFIED. IT HAS BEEN MODELED AS A DETERGENT N-OCTYLTETRAOXYETHYLENE. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 16298 / Rfactor obs: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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