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Yorodumi- PDB-5wio: TraE protein in complex with 4-(1H-pyrrol-1-yl)pyridine-2-carboxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wio | ||||||
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Title | TraE protein in complex with 4-(1H-pyrrol-1-yl)pyridine-2-carboxylic acid | ||||||
Components | Conjugal transfer protein | ||||||
Keywords | PROTEIN TRANSPORT / Type IV Secretion System / Fragment-Based Drug Design / Complex / Inhibitor / Antimicrobial Resistance / Bacterial secretion / VirB | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Casu, B. / Arya, T. / Bessette, B. / Baron, C. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Sci Rep / Year: 2017 Title: Fragment-based screening identifies novel targets for inhibitors of conjugative transfer of antimicrobial resistance by plasmid pKM101. Authors: Casu, B. / Arya, T. / Bessette, B. / Baron, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wio.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wio.ent.gz | 94.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wio_validation.pdf.gz | 477.5 KB | Display | wwPDB validaton report |
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Full document | 5wio_full_validation.pdf.gz | 497.4 KB | Display | |
Data in XML | 5wio_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 5wio_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/5wio ftp://data.pdbj.org/pub/pdb/validation_reports/wi/5wio | HTTPS FTP |
-Related structure data
Related structure data | 5wicC 5wiiC 5wipC 5i97S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18818.104 Da / Num. of mol.: 4 / Fragment: residues 70-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: traE, B634_00049, BE957_00530, ECONIH1_27615, pec386IL_00125, pEcNDM0_00049, pHKU1_33, pKC394-028, pKC396-021, pMUR050_041, pN3_023 Plasmid: PHT / Cell line (production host): BL21(DE3)STAR / Production host: Escherichia coli (E. coli) / References: UniProt: Q17U16 #2: Chemical | ChemComp-XXE / | #3: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 52.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 16% (w/v) PEG 10,000, 50 mM Bis-Tris (pH 5.5), 100 mM ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→39.478 Å / Num. obs: 26767 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rsym value: 0.151 / Net I/σ(I): 5.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I97 Resolution: 2.52→39.48 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.52→39.48 Å
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Refine LS restraints |
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LS refinement shell |
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