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Yorodumi- PDB-3f9l: Evaulaution at Atomic Resolution of the Role of Strain in Destabi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f9l | ||||||
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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: 1.19 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 | 3f9l.cif.gz | 93 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f9l.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 3f9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/3f9l ftp://data.pdbj.org/pub/pdb/validation_reports/f9/3f9l | HTTPS FTP |
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-Related structure data
Related structure data | 3f8vC 3fa0C 3fadC 1l63S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18618.457 Da / Num. of mol.: 1 / Mutation: D72A 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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-Non-polymers , 5 types, 249 molecules
#2: Chemical | ChemComp-PO4 / | ||||
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#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | #5: Chemical | ChemComp-K / | #6: 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: 2.72 Å3/Da / Density % sol: 54.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 2M Na/K Phosphate, 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: 0.82653 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 7, 2002 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82653 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→20 Å / Num. all: 58461 / Num. obs: 50477 / % possible obs: 89 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.38 / Rsym value: 0.38 / Net I/σ(I): 18.87 |
Reflection shell | Resolution: 1.19→1.24 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.6 / Num. unique all: 5496 / Rsym value: 0.36 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: 1L63 Resolution: 1.19→20 Å / Num. parameters: 14529 / Num. restraintsaints: 18092 / Cross valid method: FREE R / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.8%
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Refine analyze | Luzzati coordinate error obs: 0.06 Å / Num. disordered residues: 21 / Occupancy sum hydrogen: 1281 / Occupancy sum non hydrogen: 1507.35 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.19→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.19→1.24 Å / % reflection obs: 70.7 % |