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Yorodumi- PDB-1qtd: THE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qtd | ||||||
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Title | THE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND STABILITY OF T4 LYSOZYME | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / STRAIN / STABILITY / MUTANT / T4 LYSOZYME | ||||||
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 / Resolution: 2.5 Å | ||||||
Authors | Liu, R. / Baase, W.A. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: The introduction of strain and its effects on the structure and stability of T4 lysozyme. Authors: Liu, R. / Baase, W.A. / 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 | 1qtd.cif.gz | 45.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qtd.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qtd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/1qtd ftp://data.pdbj.org/pub/pdb/validation_reports/qt/1qtd | HTTPS FTP |
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-Related structure data
Related structure data | 1qs5C 1qs9C 1qsbC 1qtbC 1qtcC 1qthC 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
#1: Protein | Mass: 18516.234 Da / Num. of mol.: 1 / Mutation: C54T, C97A, A129W 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: M13 PHS1403 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme |
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#2: Chemical | ChemComp-HED / |
#3: 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: 2.81 Å3/Da / Density % sol: 56.23 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: potassium phosphate, sodium phosphate, BME, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: seeding / PH range low: 7.1 / PH range high: 6.3 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Mar 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→32.3 Å / Num. all: 9447 / Num. obs: 8267 / % possible obs: 87.5 % / Redundancy: 3.16 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.0572 / Net I/σ(I): 8.066 |
Reflection shell | Resolution: 2.5→2.655 Å / Redundancy: 1.69 % / Rmerge(I) obs: 0.212 / Num. unique all: 3076 / % possible all: 65.34 |
Reflection | *PLUS % possible obs: 93 % |
Reflection shell | *PLUS % possible obs: 65.3 % |
-Processing
Software |
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Refinement | Resolution: 2.5→20 Å / Stereochemistry target values: TNT PROTGEO
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||
Refine LS restraints | *PLUS
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