[English] 日本語
Yorodumi- PDB-3f8v: Evaulaution at Atomic Resolution of the Role of Strain in Destabi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f8v | ||||||
---|---|---|---|---|---|---|---|
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: 1.08 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3f8v.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3f8v.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 3f8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/3f8v ftp://data.pdbj.org/pub/pdb/validation_reports/f8/3f8v | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18643.420 Da / Num. of mol.: 1 / Mutation: 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 |
---|
-Non-polymers , 6 types, 248 molecules
#2: Chemical | ChemComp-HED / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-PO4 / | ||||||
#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-K / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.95 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 2 M Na/K Phosphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 8, 1999 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→17.9 Å / Num. all: 85136 / Num. obs: 72503 / % possible obs: 99.5 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 10.4 Å2 / Rsym value: 0.038 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.08→1.14 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 11790 / Rsym value: 0.23 / % possible all: 99.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO Starting model: l163, wild type T4 lysozyme at 1.7 Angstroms and room temp. Resolution: 1.08→17.9 Å / Num. parameters: 14302 / Num. restraintsaints: 17026 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 5%
| |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.06 Å / Num. disordered residues: 19 / Occupancy sum hydrogen: 1264.5 / Occupancy sum non hydrogen: 1535.05 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08→17.9 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.08→1.14 Å /
|