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Yorodumi- PDB-3sb8: Cu-mediated Dimer of T4 Lysozyme D61H/K65H by Synthetic Symmetrization -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sb8 | ||||||
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Title | Cu-mediated Dimer of T4 Lysozyme D61H/K65H 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: 2.65 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 | 3sb8.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sb8.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 3sb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sb8_validation.pdf.gz | 449.4 KB | Display | wwPDB validaton report |
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Full document | 3sb8_full_validation.pdf.gz | 456.2 KB | Display | |
Data in XML | 3sb8_validation.xml.gz | 19 KB | Display | |
Data in CIF | 3sb8_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/3sb8 ftp://data.pdbj.org/pub/pdb/validation_reports/sb/3sb8 | HTTPS FTP |
-Related structure data
Related structure data | 3sb5C 3sb6C 3sb7C 3sb9C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18644.348 Da / Num. of mol.: 3 / Mutation: C54T, D61H, K65H, 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: 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: 2.23 Å3/Da / Density % sol: 44.95 % |
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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: 2.65→29.441 Å / Num. obs: 14792 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.581 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 10.34 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 2.65→29.441 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8001 / SU ML: 0.69 / σ(F): 2.01 / Phase error: 26.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.276 Å2 / ksol: 0.333 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.88 Å2 / Biso mean: 27.3026 Å2 / Biso min: 8.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→29.441 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: 5
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