+Open data
-Basic information
Entry | Database: PDB / ID: 4kra | ||||||
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Title | Salmonella typhi OmpF complex with Ciprofloxacin | ||||||
Components | Outer membrane protein F | ||||||
Keywords | MEMBRANE PROTEIN / Beta barrel / Transport / Outer membrane | ||||||
Function / homology | Function and homology information porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar typhi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.32 Å | ||||||
Authors | Madhuranayaki, T. / Balasubramaniam, D. / Krishnaswamy, S. | ||||||
Citation | Journal: To be published Title: Salmonella typhi OmpF complex with Ciprofloxacin Authors: Madhuranayaki, T. / Balasubramaniam, D. / Krishnaswamy, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kra.cif.gz | 200.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kra.ent.gz | 157.8 KB | Display | PDB format |
PDBx/mmJSON format | 4kra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/4kra ftp://data.pdbj.org/pub/pdb/validation_reports/kr/4kra | HTTPS FTP |
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-Related structure data
Related structure data | 3nsgS 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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Details | Biological unit is as the same as asymmetric unit |
-Components
#1: Protein | Mass: 37887.957 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar typhi (bacteria) Strain: Ty21a / Gene: ompF / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): GJ1158 / References: UniProt: P37432*PLUS #2: Chemical | ChemComp-CPF / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN WHCIH HAS DERIVED FROM SALMONELLA TYPHI (STRAIN ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN WHCIH HAS DERIVED FROM SALMONELLA | |
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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: 3.94 Å3/Da / Density % sol: 68.77 % / Mosaicity: 1.09 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M Tri sodium citrate pH5.6, 0.25M potassium sodium tartrate, 2M Ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.32→102.358 Å / Num. all: 27234 / Num. obs: 27234 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 83.7 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 10.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 44.5 / 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: 3NSG Resolution: 3.32→50 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.844 / WRfactor Rfree: 0.3359 / WRfactor Rwork: 0.2638 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6924 / SU B: 39.362 / SU ML: 0.62 / SU Rfree: 0.6258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.626 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.78 Å2 / Biso mean: 96.5297 Å2 / Biso min: 29.72 Å2
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Refinement step | Cycle: LAST / Resolution: 3.32→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.32→3.406 Å / Rfactor Rfree error: 0.626 / Total num. of bins used: 20
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