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Yorodumi- PDB-3fad: Evaulaution at Atomic Resolution of the Role of Strain in Destabi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fad | ||||||
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Title | Evaulaution at Atomic Resolution of the Role of Strain in Destabilizing the Temperature Sensitive T4 Lysozyme Mutant Arg96-->His | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Antimicrobial / Bacteriolytic enzyme / Glycosidase / T4 lysozyme / bond angle strain / rotamer strain / temperature sensitive mutant | ||||||
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 / AB INITIO / Resolution: 1.2 Å | ||||||
Authors | Mooers, B.H.M. / Matthews, B.W. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Evaluation at atomic resolution of the role of strain in destabilizing the temperature-sensitive T4 lysozyme mutant Arg 96 --> His. Authors: Mooers, B.H. / Tronrud, D.E. / Matthews, B.W. #1: Journal: Protein Sci. / Year: 2009 Title: Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme. Authors: Mooers, B.H. / Baase, W.A. / Wray, J.W. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fad.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fad.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 3fad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/3fad ftp://data.pdbj.org/pub/pdb/validation_reports/fa/3fad | HTTPS FTP |
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-Related 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: 18599.410 Da / Num. of mol.: 1 / Mutation: D72A/R96H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: gene e / Plasmid: PHS1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme | ||||
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#2: Chemical | #3: Chemical | ChemComp-BME / | #4: 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: 2.73 Å3/Da / Density % sol: 54.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 2 M Na/K Phospahte, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 23, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→19.7 Å / Num. all: 63952 / Num. obs: 62568 / % possible obs: 99.7 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 14.66 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 12.83 |
Reflection shell | Resolution: 1.2→1.25 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.3 / Num. unique all: 7330 / Rsym value: 0.33 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.2→19.7 Å / Num. parameters: 14355 / Num. restraintsaints: 17953 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4.9%
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Refine analyze | Num. disordered residues: 32 / Occupancy sum hydrogen: 1233.4 / Occupancy sum non hydrogen: 1497.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→19.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.25 Å / Num. reflection obs: 5557 |