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Yorodumi- PDB-2xg6: Molecular insights into clinically isolated OmpC mutants and thei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xg6 | ||||||
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Title | Molecular insights into clinically isolated OmpC mutants and their role in multi-drug resistance | ||||||
Components | OMPC | ||||||
Keywords | TRANSPORT PROTEIN / PORIN | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 Å | ||||||
Authors | Lou, H. / Naismith, J.H. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Altered Antibiotic Transport in Ompc Mutants Isolated from a Series of Clinical Strains of Multi-Drug Resistant E. Coli. Authors: Lou, H. / Chen, M. / Black, S.S. / Bushell, S.R. / Ceccarelli, M. / Mach, T. / Beis, K. / Low, A.S. / Bamford, V.A. / Booth, I.R. / Bayley, H. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xg6.cif.gz | 397.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xg6.ent.gz | 331 KB | Display | PDB format |
PDBx/mmJSON format | 2xg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xg6_validation.pdf.gz | 500.7 KB | Display | wwPDB validaton report |
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Full document | 2xg6_full_validation.pdf.gz | 561.5 KB | Display | |
Data in XML | 2xg6_validation.xml.gz | 70.4 KB | Display | |
Data in CIF | 2xg6_validation.cif.gz | 93.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/2xg6 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xg6 | HTTPS FTP |
-Related structure data
Related structure data | 2xe1SC 2xe2C 2xe3C 2xe5C 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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Unit cell |
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-Components
#1: Protein | Mass: 38337.273 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O6 / Description: DERIVED FROM O6 UROPATHOGENIC STRAIN / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9K597 #2: Chemical | Sequence details | NOTE THIS CLINICAL ISOLATE HAS MUTANTS D18E, S271F, R124H | |
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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: 3.5 Å3/Da / Density % sol: 69.87 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 3.47→54 Å / Num. obs: 40939 / % possible obs: 84.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 94 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 3.47→3.7 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XE1 Resolution: 3.47→53.19 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.862 / SU B: 87.244 / SU ML: 0.566 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.717 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. THIS USED NEW REFMAC5 (V5.6) OPTION NSCR LOCAL.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.027 Å2
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Refinement step | Cycle: LAST / Resolution: 3.47→53.19 Å
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Refine LS restraints |
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