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Yorodumi- PDB-1pho: CRYSTAL STRUCTURES EXPLAIN FUNCTIONAL PROPERTIES OF TWO E. COLI PORINS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pho | ||||||
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Title | CRYSTAL STRUCTURES EXPLAIN FUNCTIONAL PROPERTIES OF TWO E. COLI PORINS | ||||||
Components | PHOSPHOPORIN | ||||||
Keywords | OUTER MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Schirmer, T. / Cowan, S.W. / Jansonius, J.N. | ||||||
Citation | Journal: Nature / Year: 1992 Title: Crystal structures explain functional properties of two E. coli porins. Authors: Cowan, S.W. / Schirmer, T. / Rummel, G. / Steiert, M. / Ghosh, R. / Pauptit, R.A. / Jansonius, J.N. / Rosenbusch, J.P. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Trigonal Crystals of Porin from Escherichia Coli Authors: Pauptit, R.A. / Zhang, H. / Rummel, G. / Schirmer, T. / Jansonius, J.N. / Rosenbusch, J.P. #2: Journal: J.Struct.Biol. / Year: 1991 Title: A Common Channel-Forming Motif in Evolutionarily Distant Porins Authors: Pauptit, R.A. / Schirmer, T. / Jansonius, J.N. / Rosenbusch, J.P. / Parker, M.W. / Tucker, A.D. / Tsernoglou, D. / Weiss, M.S. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pho.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pho.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/1pho ftp://data.pdbj.org/pub/pdb/validation_reports/ph/1pho | 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: THE FOLLOWING RESIDUES COULD NOT BE MODELLED DUE TO WEAK OR NONEXISTENT ELECTRON DENSITY AND ARE INCLUDED IN THE MODEL IN AN ARBITRARY CONFORMATION ONLY FOR CONVENIENCE: ASP 25, ASN 26, ALA 32, ...1: THE FOLLOWING RESIDUES COULD NOT BE MODELLED DUE TO WEAK OR NONEXISTENT ELECTRON DENSITY AND ARE INCLUDED IN THE MODEL IN AN ARBITRARY CONFORMATION ONLY FOR CONVENIENCE: ASP 25, ASN 26, ALA 32, SER 33, ASP 181, PHE 182, GLY 183, ASP 184, ASN 198, GLU 199, SER 204, GLY 249, ASP 319, SER 320, AND ASP 321. |
-Components
#1: Protein | Mass: 36871.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P02932 |
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Sequence details | THESE COORDINATES ARE IN AN INTERMEDIATE STAGE OF REFINEMENT AND WILL BE UPDATED SOON. THE RESIDUE ...THESE COORDINATE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.88 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 9.8 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3 Å / Num. obs: 8685 / % possible obs: 95 % / Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Resolution: 3→8 Å / Rfactor Rwork: 0.222 / Rfactor obs: 0.222 Details: ATOMS THAT ARE NOT WELL DEFINED DUE TO POOR ELECTRON DENSITY HAVE A WEIGHT OF ZERO. THE FOLLOWING RESIDUES COULD NOT BE MODELLED DUE TO WEAK OR NONEXISTENT ELECTRON DENSITY AND ARE INCLUDED ...Details: ATOMS THAT ARE NOT WELL DEFINED DUE TO POOR ELECTRON DENSITY HAVE A WEIGHT OF ZERO. THE FOLLOWING RESIDUES COULD NOT BE MODELLED DUE TO WEAK OR NONEXISTENT ELECTRON DENSITY AND ARE INCLUDED IN THE MODEL IN AN ARBITRARY CONFORMATION ONLY FOR CONVENIENCE: 25-33 181-184 198-199 204 249 319-321 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 8 Å / Rfactor obs: 0.222 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.9 |