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Yorodumi- PDB-8qxp: Crystal structure of the outer membrane porin OmpW from Klebsiell... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qxp | ||||||
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Title | Crystal structure of the outer membrane porin OmpW from Klebsiella pneumoniae | ||||||
Components | OmpW protein | ||||||
Keywords | MEMBRANE PROTEIN / outer membrane porin | ||||||
Function / homology | Outer membrane protein, OmpW / OmpW family / outer membrane / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / OmpW protein Function and homology information | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Seddon, C. / Beis, K. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2024 Title: Structure of the outer membrane porin OmpW from the pervasive pathogen Klebsiella pneumoniae. Authors: Seddon, C. / Frankel, G. / Beis, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qxp.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qxp.ent.gz | 33.2 KB | Display | PDB format |
PDBx/mmJSON format | 8qxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qxp_validation.pdf.gz | 430.1 KB | Display | wwPDB validaton report |
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Full document | 8qxp_full_validation.pdf.gz | 430.8 KB | Display | |
Data in XML | 8qxp_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 8qxp_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/8qxp ftp://data.pdbj.org/pub/pdb/validation_reports/qx/8qxp | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20778.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: sequence of mature protein / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ompW, BN49_2384, KPZU09_20550 / Production host: Escherichia coli (E. coli) / References: UniProt: W9B759 | ||
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#2: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.35 M lithium sulphate, 0.1 M sodium acetate pH 4.0, 11% PEG 600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→52.97 Å / Num. obs: 5639 / % possible obs: 99.84 % / Redundancy: 12.7 % / Biso Wilson estimate: 98.04 Å2 / CC1/2: 0.855 / Net I/σ(I): 64 |
Reflection shell | Resolution: 3.2→3.315 Å / Num. unique obs: 560 / CC1/2: 0.998 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→52.97 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→52.97 Å
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Refine LS restraints |
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LS refinement shell |
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