+Open data
-Basic information
Entry | Database: PDB / ID: 2b70 | ||||||
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Title | T4 Lysozyme mutant L99A at ambient pressure | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / High Pressure / T4 Lysozyme / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
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 / Resolution: 2.4 Å | ||||||
Authors | Collins, M.D. / Quillin, M.L. / Matthews, B.W. / Gruner, S.M. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation Authors: Collins, M.D. / Hummer, G. / Quillin, M.L. / Matthews, B.W. / Gruner, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b70.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b70.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 2b70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b70_validation.pdf.gz | 433.1 KB | Display | wwPDB validaton report |
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Full document | 2b70_full_validation.pdf.gz | 433.6 KB | Display | |
Data in XML | 2b70_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 2b70_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/2b70 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/2b70 | HTTPS FTP |
-Related structure data
Related structure data | 2b6wC 2b6xC 2b6yC 2b6zC 2b72C 2b73C 2b74C 2b75C 2oe4C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18359.023 Da / Num. of mol.: 1 / Mutation: C54T,C97A,L99A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: E / Plasmid: PHS1403 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: ~ 2.0 M Na/K phosphate, 50 mM beta-mercaptoethanol, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9174 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2004 / Details: mirrors |
Radiation | Monochromator: Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→52.78 Å / Num. all: 7969 / Num. obs: 7969 / % possible obs: 98.08 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.073 |
Reflection shell | Resolution: 2.4→2.462 Å / % possible all: 99.35 |
-Processing
Software |
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Refinement | Resolution: 2.4→52.78 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.982 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.153 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→52.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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