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Yorodumi- PDB-1lw9: Multiple methionine substitutions are tolerated in T4 lysozyme an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lw9 | ||||||
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Title | Multiple methionine substitutions are tolerated in T4 lysozyme and have coupled effects on folding and stability | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / hydrolase (o-glycosyl) / T4 lysozyme / methionine core mutant / protein engineering / protein folding | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Gassner, N.C. / Baase, W.A. / Mooers, B.H.M. / Busam, R.D. / Weaver, L.H. / Lindstrom, J.D. / Quillin, M.L. / Matthews, B.W. | ||||||
Citation | Journal: Biophys.Chem. / Year: 2003 Title: Multiple methionine substitutions are tolerated in T4 lysozyme and have coupled effects on folding and stability. Authors: Gassner, N.C. / Baase, W.A. / Mooers, B.H. / Busam, R.D. / Weaver, L.H. / Lindstrom, J.D. / Quillin, M.L. / 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 | 1lw9.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lw9.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lw9_validation.pdf.gz | 440 KB | Display | wwPDB validaton report |
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Full document | 1lw9_full_validation.pdf.gz | 444.4 KB | Display | |
Data in XML | 1lw9_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1lw9_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/1lw9 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/1lw9 | HTTPS FTP |
-Related structure data
Related structure data | 1ks3C 1kw5C 1kw7C 1ky0C 1ky1C 1l0jC 1l0kC 1lpyC 1lwgC 1lwkC 1l63S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18628.363 Da / Num. of mol.: 1 / Mutation: C54T,C97A 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 / Plasmid: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme | ||||
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#2: Chemical | ChemComp-K / | ||||
#3: Chemical | #4: Chemical | ChemComp-HED / | #5: 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: 2.68 Å3/Da / Density % sol: 53.8 % Description: 1) Working and test sets were not combined during the last cycles of refinement. 2) OVERALL B-VALUES: B11=B12=B22=2.5 B33=-4.99 B13=B23=0.00 |
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Crystal grow | pH: 6.7 / Details: pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 14, 2002 / Details: MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→27.1 Å / Num. obs: 35919 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.316 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L63 Resolution: 1.45→23 Å / Isotropic thermal model: TNT BCORRELATION LIBRARY / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT'S TNTGEO_V010.DAT Details: THE USE OF RFREE FOR THIS STRUCTURE during refinement was not very valid since the starting model had been refined against 1.75 Angstrom room temperature data (~15000 reflections). ...Details: THE USE OF RFREE FOR THIS STRUCTURE during refinement was not very valid since the starting model had been refined against 1.75 Angstrom room temperature data (~15000 reflections). Nonetheless, for the benefit of future workers, this structure (1LW9) was NOT refined against both the test and working sets during the final stage of refinement.
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Solvent computation | Solvent model: TNT'S MODEL / Bsol: 232.25 Å2 / ksol: 0.86 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.45→23 Å
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Refine LS restraints |
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