+Open data
-Basic information
Entry | Database: PDB / ID: 5khz | ||||||
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Title | PSEUDO T4 LYSOZYME | ||||||
Components | Endolysin | ||||||
Keywords | HYDROLASE / HALOGEN BONDS / 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 / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Scholfield, M.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2017 Title: Structure-Energy Relationships of Halogen Bonds in Proteins. Authors: Scholfield, M.R. / Ford, M.C. / Carlsson, A.C. / Butta, H. / Mehl, R.A. / Ho, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5khz.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5khz.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 5khz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5khz_validation.pdf.gz | 414.2 KB | Display | wwPDB validaton report |
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Full document | 5khz_full_validation.pdf.gz | 414.8 KB | Display | |
Data in XML | 5khz_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 5khz_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/5khz ftp://data.pdbj.org/pub/pdb/validation_reports/kh/5khz | HTTPS FTP |
-Related structure data
Related structure data | 5ki1C 5ki2C 5ki3C 5ki8C 5kigC 5kiiC 5kimC 5kioC 1l63S C: citing same article (ref.) 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: 19457.246 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / 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: 2.75 Å3/Da / Density % sol: 55.21 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 2.0M KPO4, 50MM 2-HYDROXYETHYLDISULFIDE, 50MM 2-MERCAPTOETHANOL, PH 6.9 PH range: 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→21.98 Å / Num. obs: 31370 / % possible obs: 92 % / Redundancy: 9.5 % / Biso Wilson estimate: 11.77 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.089 / Net I/σ(I): 28.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L63 Resolution: 1.49→21.98 Å / SU ML: 0.133 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.276
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→21.98 Å
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Refine LS restraints |
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LS refinement shell |
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