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Yorodumi- PDB-6h4b: A polyamorous repressor: deciphering the evolutionary strategy us... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h4b | |||||||||||||||||||||
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Title | A polyamorous repressor: deciphering the evolutionary strategy used by the phage-inducible chromosomal islands to spread in nature. | |||||||||||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Complex | |||||||||||||||||||||
Function / homology | Function and homology information | |||||||||||||||||||||
Biological species | Staphylococcus virus 69 Staphylococcus aureus (bacteria) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 Å | |||||||||||||||||||||
Authors | Ciges-Tomas, J.R. / Alite, C. / Bowring, J.Z. / Donderis, J. / Penades, J.R. / Marina, A. | |||||||||||||||||||||
Funding support | Spain, United Kingdom, 6items
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Citation | Journal: Nat Commun / Year: 2019 Title: The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature. Authors: Rafael Ciges-Tomas, J. / Alite, C. / Humphrey, S. / Donderis, J. / Bowring, J. / Salvatella, X. / Penades, J.R. / Marina, A. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h4b.cif.gz | 59.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h4b.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 6h4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h4b_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
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Full document | 6h4b_full_validation.pdf.gz | 443 KB | Display | |
Data in XML | 6h4b_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 6h4b_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/6h4b ftp://data.pdbj.org/pub/pdb/validation_reports/h4/6h4b | HTTPS FTP |
-Related structure data
Related structure data | 6h48SC 6h49C 6h4cC 5milS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22895.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus virus 69 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4ZDP4 |
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#2: Protein | Mass: 11535.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F0J8 |
#3: 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: 2.25 Å3/Da / Density % sol: 45.24 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 10%PEG4000, 10%isopropanol, 0.1MNa-Citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→86.9 Å / Num. obs: 7002 / % possible obs: 100 % / Redundancy: 33.3 % / CC1/2: 1 / Rmerge(I) obs: 0.099 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 33.4 % / Rmerge(I) obs: 1.038 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1110 / CC1/2: 0.913 / Rpim(I) all: 0.183 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Chain A, 5MIL, chain B 6H48 Resolution: 2.902→61.448 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 32.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.902→61.448 Å
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Refine LS restraints |
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LS refinement shell |
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