+Open data
-Basic information
Entry | Database: PDB / ID: 6u0b | ||||||
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Title | Neutron crystal structure of wtT4LD | ||||||
Components | EndolysinLysin | ||||||
Keywords | HYDROLASE / T4 Lysozyme / cavity | ||||||
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 / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.951 Å | ||||||
Authors | Cuneo, M.J. / Myles, D.A. / Li, L. | ||||||
Citation | Journal: To be published Title: Solvent entry into cavities of T4 lysozyme. Authors: Li, L. / Myles, D.A. / Cuneo, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u0b.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u0b.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 6u0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/6u0b ftp://data.pdbj.org/pub/pdb/validation_reports/u0/6u0b | HTTPS FTP |
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-Related structure data
Related structure data | 6u0cC 6u0fC 5vnqS 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
#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) / Gene: e, T4Tp126 / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: P00720*PLUS, lysozyme |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: ~2.0 M Na/K phosphate, pH 6-7, 250 mM NaCl |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Entry-ID: 6U0B
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Reflection shell |
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-Processing
Software |
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Refinement | % reflection Rfree: 4.97 % / SU ML: 0.19 / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 19.88 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5VNQ
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Refinement step | Cycle: final / Resolution: 1.951→35 Å
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LS refinement shell | Rfactor Rfree error: 0
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