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Yorodumi- PDB-6zhv: Crystal structure of OmpF porin soaked in ciprofloxacin metaloant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zhv | ||||||
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Title | Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic | ||||||
Components | Outer membrane porin F | ||||||
Keywords | MEMBRANE PROTEIN / OmpF / porin | ||||||
Function / homology | Function and homology information colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport / monoatomic ion channel activity / lipid binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.945 Å | ||||||
Authors | Sousa, C.F. / Morais-Cabral, J. / Gameiro, P. | ||||||
Funding support | Portugal, 1items
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Citation | Journal: To Be Published Title: Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic Authors: Sousa, C.F. / Morais-Cabral, J. / Gameiro, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zhv.cif.gz | 219.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zhv.ent.gz | 175.8 KB | Display | PDB format |
PDBx/mmJSON format | 6zhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/6zhv ftp://data.pdbj.org/pub/pdb/validation_reports/zh/6zhv | HTTPS FTP |
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-Related structure data
Related structure data | 6zhpC 4lsfS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 39365.043 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: ompF, cmlB, coa, cry, tolF, b0929, JW0912 / Plasmid: pRSF-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02931 #2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-QLB / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.4 Å3/Da / Density % sol: 48.81 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 50% PEG 200, 0.2 M MgCl2, 0.1 M NaCacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98013 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.945→45.68 Å / Num. obs: 83824 / % possible obs: 99.5 % / Redundancy: 13.5 % / Biso Wilson estimate: 34.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.029 / Rrim(I) all: 0.109 / Net I/σ(I): 15 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LSF Resolution: 1.945→45.296 Å / FOM work R set: 0.8354 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.43 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.43 Å2 / Biso mean: 29.66 Å2 / Biso min: 12.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.945→45.296 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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