+Open data
-Basic information
Entry | Database: PDB / ID: 6v51 | |||||||||||||||
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Title | Spin-labeled T4 Lysozyme (9/131FnbY)-(4-Amino-TEMPO) | |||||||||||||||
Components | EndolysinLysin | |||||||||||||||
Keywords | HYDROLASE / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||||||||
Authors | Liu, J. / Morizumi, T. / Ou, W.L. / Wang, L. / Ernst, O.P. | |||||||||||||||
Funding support | United States, Canada, 4items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Genetically Encoded Quinone Methides Enabling Rapid, Site-Specific, and Photocontrolled Protein Modification with Amine Reagents. Authors: Liu, J. / Cheng, R. / Van Eps, N. / Wang, N. / Morizumi, T. / Ou, W.L. / Klauser, P.C. / Rozovsky, S. / Ernst, O.P. / Wang, L. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v51.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v51.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 6v51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/6v51 ftp://data.pdbj.org/pub/pdb/validation_reports/v5/6v51 | HTTPS FTP |
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-Related structure data
Related structure data | 1p2lS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18756.447 Da / Num. of mol.: 1 / Mutation: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126 Production host: Escherichia coli str. K-12 substr. DH10B (bacteria) References: UniProt: D9IEF7, lysozyme | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: sodium/potassium phosphate, sodium chloride, hexane-1,6-diol, 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→31.83 Å / Num. obs: 31896 / % possible obs: 99.97 % / Redundancy: 2 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01 / Rpim(I) all: 0.01 / Rrim(I) all: 0.01309 / Net I/σ(I): 40.17 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 2 % / Rmerge(I) obs: 0.043 / Num. unique obs: 3148 / CC1/2: 0.994 / Rpim(I) all: 0.043 / Rrim(I) all: 0.061 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P2L Resolution: 1.5→31.83 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 15.31 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→31.83 Å
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Refine LS restraints |
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