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Yorodumi- PDB-1xju: Crystal structure of secreted inactive form of P1 phage endolysin Lyz -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xju | ||||||
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Title | Crystal structure of secreted inactive form of P1 phage endolysin Lyz | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / secreted inactive conformation | ||||||
Function / homology | Function and homology information peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / host cell plasma membrane / membrane Similarity search - Function | ||||||
Biological species | Enterobacteria phage P1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å | ||||||
Authors | Arockiasamy, A. / Sacchettini, J.C. | ||||||
Citation | Journal: Science / Year: 2005 Title: Disulfide isomerization after membrane release of its SAR domain activates P1 lysozyme. Authors: Xu, M. / Arulandu, A. / Struck, D.K. / Swanson, S. / Sacchettini, J.C. / Young, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xju.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xju.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 1xju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xju_validation.pdf.gz | 380.5 KB | Display | wwPDB validaton report |
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Full document | 1xju_full_validation.pdf.gz | 381.4 KB | Display | |
Data in XML | 1xju_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 1xju_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/1xju ftp://data.pdbj.org/pub/pdb/validation_reports/xj/1xju | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 18478.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: 17, LYSA, LyZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q37875, lysozyme #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.7 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion / pH: 4.5 Details: sodium acetate, PEG4000, pH 4.5, VAPOR DIFFUSION, temperature 291.15K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.07→50 Å / Num. obs: 116001 / % possible obs: 90.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.057 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→46.62 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.029 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.07→46.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.07→1.098 Å / Total num. of bins used: 20 /
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