+Open data
-Basic information
Entry | Database: PDB / ID: 3fi5 | ||||||
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Title | Crystal Structure of T4 Lysozyme Mutant R96W | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Antimicrobial / Bacteriolytic enzyme / Glycosidase / T4 lysozyme / electrostatics / strain / protein stability | ||||||
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 / Resolution: 1.53 Å | ||||||
Authors | Mooers, B.H.M. / Matthews, B.W. | ||||||
Citation | 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. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fi5.cif.gz | 305.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fi5.ent.gz | 246.9 KB | Display | PDB format |
PDBx/mmJSON format | 3fi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fi5_validation.pdf.gz | 470.8 KB | Display | wwPDB validaton report |
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Full document | 3fi5_full_validation.pdf.gz | 484.5 KB | Display | |
Data in XML | 3fi5_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 3fi5_validation.cif.gz | 58.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/3fi5 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/3fi5 | HTTPS FTP |
-Related structure data
Related structure data | 3c7wC 3c7yC 3c7zC 3c80C 3c81C 3c82C 3c83C 3c8qC 3c8rC 3c8sC 3cdoC 3cdqC 3cdrC 3cdtC 3cdvC 1lw9S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 18691.482 Da / Num. of mol.: 4 / Mutation: R96W 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 #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-IPA / | #5: 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: 2.26 Å3/Da / Density % sol: 45.66 % |
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-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: May 29, 1999 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→18.804 Å / Num. all: 101134 / Num. obs: 92759 / % possible obs: 70.2 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 12.42 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 19.96 |
Reflection shell | Resolution: 1.53→1.57 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 5.15 / Num. unique all: 3111 / Rsym value: 0.195 / % possible all: 41.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LW9 Resolution: 1.53→18.804 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.343 Å2 / ksol: 0.408 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→18.804 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: 17
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