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Yorodumi- PDB-1t8g: Crystal structure of phage T4 lysozyme mutant L32A/L33A/T34A/C54T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t8g | ||||||
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Title | Crystal structure of phage T4 lysozyme mutant L32A/L33A/T34A/C54T/C97A/E108V | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / lysozyme / poly-alanine | ||||||
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: 1.8 Å | ||||||
Authors | He, M.M. / Wood, Z.A. / Baase, W.A. / Xiao, H. / Matthews, B.W. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: Alanine-scanning mutagenesis of the beta-sheet region of phage T4 lysozyme suggests that tertiary context has a dominant effect on beta-sheet formation. Authors: He, M.M. / Wood, Z.A. / Baase, W.A. / Xiao, H. / 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 | 1t8g.cif.gz | 48.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t8g.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 1t8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t8g_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 1t8g_full_validation.pdf.gz | 448 KB | Display | |
Data in XML | 1t8g_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 1t8g_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/1t8g ftp://data.pdbj.org/pub/pdb/validation_reports/t8/1t8g | HTTPS FTP |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18514.219 Da / Num. of mol.: 1 / Mutation: L32A,L33A,T34A,E108V,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 / Gene: E / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme | ||||
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#2: Chemical | ChemComp-PO4 / | ||||
#3: Chemical | #4: Chemical | ChemComp-BME / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.2 % |
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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: 1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30.4 Å / Num. obs: 16520 / % possible obs: 97.7 % / Redundancy: 8.3 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.034 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 8.7 / Rsym value: 0.083 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3428991.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.61 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→30.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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