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Yorodumi- PDB-177l: Protein flexibility and adaptability seen in 25 crystal forms of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 177l | ||||||
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Title | Protein flexibility and adaptability seen in 25 crystal forms of T4 LYSOZYME | ||||||
Components | T4 LYSOZYME | ||||||
Keywords | HYDROLASE / HYDROLASE (O-GLYCOSYL) | ||||||
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 | Bacteriophage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Matsumura, M. / Weaver, L. / Zhang, X.-J. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. Authors: Zhang, X.J. / Wozniak, J.A. / Matthews, B.W. #1: Journal: J.Mol.Biol. / Year: 1987 Title: Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution Authors: Weaver, L.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 | 177l.cif.gz | 43.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb177l.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 177l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 177l_validation.pdf.gz | 416 KB | Display | wwPDB validaton report |
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Full document | 177l_full_validation.pdf.gz | 429.3 KB | Display | |
Data in XML | 177l_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 177l_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/77/177l ftp://data.pdbj.org/pub/pdb/validation_reports/77/177l | HTTPS FTP |
-Related structure data
Related structure data | 167lC 168lC 169lC 170lC 171lC 172lC 173lC 174lC 175lC 176lC 178lC 180lC 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: 18562.367 Da / Num. of mol.: 1 / Mutation: C54T, C97A, D127C, R154C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteriophage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: E / Plasmid: M13 / References: UniProt: P00720, lysozyme |
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#2: 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: 2.92 Å3/Da / Density % sol: 57.83 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.6 / Details: pH 8.6 | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 58 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 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: Dec 29, 1993 |
Radiation | Monochromator: Graphite / 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→20 Å / Num. obs: 7778 / % possible obs: 97 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / σ(F): 0 Details: MUTANT SPACE GROUP, P 4(2)22, IS NON-ISOMORPHOUS TO WILD TYPE. STARTING COORDINATES WERE BASED ON THE WILD TYPE STRUCTURE.
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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