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Yorodumi- PDB-3sb9: Cu-mediated Dimer of T4 Lysozyme R76H/R80H by Synthetic Symmetrization -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sb9 | ||||||
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Title | Cu-mediated Dimer of T4 Lysozyme R76H/R80H by Synthetic Symmetrization | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / metal-mediated synthetic symmetrization / synthetic symmetrization | ||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å | ||||||
Authors | Soriaga, A.B. / Laganowsky, A. / Zhao, M. / Sawaya, M.R. / Cascio, D. / Yeates, T.O. | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: An approach to crystallizing proteins by metal-mediated synthetic symmetrization. Authors: Laganowsky, A. / Zhao, M. / Soriaga, A.B. / Sawaya, M.R. / Cascio, D. / Yeates, T.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sb9.cif.gz | 147.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sb9.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 3sb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sb9_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
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Full document | 3sb9_full_validation.pdf.gz | 448.1 KB | Display | |
Data in XML | 3sb9_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 3sb9_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/3sb9 ftp://data.pdbj.org/pub/pdb/validation_reports/sb/3sb9 | HTTPS FTP |
-Related structure data
Related structure data | 3sb5C 3sb6C 3sb7C 3sb8C 3sbaC 3sbbC 3serC 3sesC 3setC 3seuC 3sevC 3sewC 3sexC 3seyC 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
#1: Protein | Mass: 18574.229 Da / Num. of mol.: 2 / Mutation: C54T, R76H, R80H, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P00720, lysozyme #2: Chemical | #3: Chemical | ChemComp-CU / | #4: 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: 3.68 Å3/Da / Density % sol: 66.58 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 3.5M Sodium Formate, pH 7.0, vapor diffusion, hanging drop, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→80 Å / Num. obs: 19881 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→79.114 Å / Occupancy max: 1 / Occupancy min: 0.34 / SU ML: 0.74 / σ(F): 0 / Phase error: 25.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.893 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.45→79.114 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 18.3847 Å / Origin y: 20.53 Å / Origin z: -0.5173 Å
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Refinement TLS group | Selection details: ALL |