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Yorodumi- PDB-4ht4: Molecular Basis of Vancomycin Resistance Transfer in Staphylococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ht4 | ||||||
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Title | Molecular Basis of Vancomycin Resistance Transfer in Staphylococcus aureus | ||||||
Components |
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Keywords | Hydrolase/DNA / vancomycin resistance plasmid / DNA relaxase / S. aureus / conjugative transfer / DNA hairpin / Hydrolase-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.907 Å | ||||||
Authors | Edwards, J.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus. Authors: Edwards, J.S. / Betts, L. / Frazier, M.L. / Pollet, R.M. / Kwong, S.M. / Walton, W.G. / Ballentine, W.K. / Huang, J.J. / Habibi, S. / Del Campo, M. / Meier, J.L. / Dervan, P.B. / Firth, N. / Redinbo, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ht4.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ht4.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ht4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/4ht4 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/4ht4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / DNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 23069.264 Da / Num. of mol.: 1 / Mutation: F25Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nes, NES from pLW1043 / Plasmid: pCPD-lasso / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI / References: UniProt: Q53632 |
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#2: DNA chain | Mass: 8640.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oriT DNA hairpin |
-Non-polymers , 4 types, 29 molecules
#3: Chemical | ChemComp-NI / | ||||
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#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16% PEG 8,000, 120 mM calcium acetate, 80 mM sodium cacolydate, and 20% glycerol v/v , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH ANOMALOUS / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 20.3 % / Av σ(I) over netI: 47.95 / Number: 179546 / Rmerge(I) obs: 0.097 / Χ2: 2.15 / D res high: 2.9 Å / D res low: 100 Å / Num. obs: 8865 / % possible obs: 97.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.9→100 Å / Num. obs: 8865 / % possible obs: 97.7 % / Redundancy: 20.3 % / Rmerge(I) obs: 0.097 / Χ2: 2.15 / Net I/σ(I): 11.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.907→48.509 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7129 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 32.11 / 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: 148.36 Å2 / Biso mean: 75.774 Å2 / Biso min: 27.62 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.907→48.509 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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