+Open data
-Basic information
Entry | Database: PDB / ID: 1osm | ||||||
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Title | OSMOPORIN (OMPK36) FROM KLEBSIELLA PNEUMONIAE | ||||||
Components | OMPK36 | ||||||
Keywords | OUTER MEMBRANE PROTEIN / NON-SPECIFIC PORIN / OSMOPORIN / BETA-BARREL / TRANSMEMBRANE | ||||||
Function / homology | Function and homology information porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Dutzler, R. / Schirmer, T. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Crystal structure and functional characterization of OmpK36, the osmoporin of Klebsiella pneumoniae. Authors: Dutzler, R. / Rummel, G. / Alberti, S. / Hernandez-Alles, S. / Phale, P. / Rosenbusch, J. / Benedi, V. / Schirmer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1osm.cif.gz | 200 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1osm.ent.gz | 165.2 KB | Display | PDB format |
PDBx/mmJSON format | 1osm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/1osm ftp://data.pdbj.org/pub/pdb/validation_reports/os/1osm | HTTPS FTP |
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-Related structure data
Related structure data | 2omfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 37630.477 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q48473 #2: Chemical | ChemComp-D12 / Sequence details | THE RESIDUE NUMBERING IS BASED ON THE HOMOLOGOUS MATRIX PORIN FROM E.COLI (OMPF, PDB CODE 2OMF). ...THE RESIDUE NUMBERING IS BASED ON THE HOMOLOGOUS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9.8 / Details: pH 9.8 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.94 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→15 Å / Num. obs: 47412 / % possible obs: 96.1 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 3.2→3.31 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / % possible all: 97.2 |
Reflection shell | *PLUS % possible obs: 97.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OMF Resolution: 3.2→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: STRICT NCS COORDINATE AND B-FACTOR CONSTRAINTS USED FOR THE 6 PROTEIN CHAINS IN THE ASYMMETRIC UNITS. THE TWO GROUPS OF DETERGENTS (MODELED AS 2X9 DODECANE MOLECULES) WERE REFINED WITH 2- ...Details: STRICT NCS COORDINATE AND B-FACTOR CONSTRAINTS USED FOR THE 6 PROTEIN CHAINS IN THE ASYMMETRIC UNITS. THE TWO GROUPS OF DETERGENTS (MODELED AS 2X9 DODECANE MOLECULES) WERE REFINED WITH 2-FOLD STRICT NCS CONSTRAINTS. ONE GROUP B-FACTOR PER DETERGENT MOLECULE.
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Displacement parameters | Biso mean: 55.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT NCS CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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