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Yorodumi- PDB-5xpf: High-resolution X-ray structure of the T26H mutant of T4 lysozyme -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xpf | |||||||||
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Title | High-resolution X-ray structure of the T26H mutant of T4 lysozyme | |||||||||
Components | EndolysinLysin | |||||||||
Keywords | HYDROLASE / Alpha and beta protein / T26H mutant / Perdeuterated protein | |||||||||
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: 1.04 Å | |||||||||
Authors | Hiromoto, T. / Kuroki, R. | |||||||||
Citation | Journal: Protein Sci. / Year: 2017 Title: Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type. Authors: Hiromoto, T. / Meilleur, F. / Shimizu, R. / Shibazaki, C. / Adachi, M. / Tamada, T. / Kuroki, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xpf.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xpf.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/5xpf ftp://data.pdbj.org/pub/pdb/validation_reports/xp/5xpf | HTTPS FTP |
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-Related structure data
Related structure data | 5xpeC 1qt8S 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: 18665.406 Da / Num. of mol.: 1 / Mutation: T26H, C54T, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D9IEF7, UniProt: P00720*PLUS, lysozyme |
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-Non-polymers , 5 types, 257 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-HEZ / #5: Chemical | #6: 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: 2.65 Å3/Da / Density % sol: 53.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Sodium-potassium phosphate, Sodium chloride, 1,6-Hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.8 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2014 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→50 Å / Num. obs: 95774 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.019 / Rrim(I) all: 0.045 / Rsym value: 0.041 / Χ2: 2.263 / Net I/av σ(I): 51.6 / Net I/σ(I): 51.6 |
Reflection shell | Resolution: 1.04→1.08 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 9481 / CC1/2: 0.886 / Rpim(I) all: 0.215 / Rrim(I) all: 0.422 / Rsym value: 0.361 / Χ2: 1.732 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QT8 Resolution: 1.04→45.58 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Details: ANISOTROPIC REFINEMENT REDUCED FREE R
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Displacement parameters | Biso max: 96.95 Å2 / Biso mean: 18.1199 Å2 / Biso min: 7.69 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.04→45.58 Å
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Refine LS restraints |
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