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Yorodumi- PDB-2j8f: Crystal structure of the modular Cpl-1 endolysin complexed with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j8f | |||||||||
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Title | Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (E94Q mutant in complex with a disaccharide- pentapeptide) | |||||||||
Components | LYSOZYME | |||||||||
Keywords | HYDROLASE / ANTIMICROBIAL / MUEIN HYDROLASE / BACTERIOLYTIC ENZYME / PNEUMOCOCCAL CELL WALL DEGRADATION / LYSOZYME / GLYCOSIDASE / MULTIMODULAR | |||||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to bacterium Similarity search - Function | |||||||||
Biological species | BACTERIOPHAGE CP-1 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | |||||||||
Authors | Perez-Dorado, I. / Hermoso, J.A. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Elucidation of the Molecular Recognition of Bacterial Cell Wall by Modular Pneumococcal Phage Endolysin Cpl-1. Authors: Perez-Dorado, I. / Campillo, N.E. / Monterroso, B. / Hesek, D. / Lee, M. / Paez, J.A. / Garcia, P. / Martinez-Ripoll, M. / Garcia, J.L. / Mobashery, S. / Menendez, M. / Hermoso, J.A. #1: Journal: Structure / Year: 2003 Title: Structural Basis for Selective Recognition of Pneumococcal Cell Wall by Modular Endolysin from Phage Cp-1 Authors: Hermoso, J.A. / Monterroso, B. / Albert, A. / Galan, B. / Ahrazem, O. / Garcia, P. / Martinez-Ripoll, M. / Garcia, J.L. / Menendez, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Complete Modular Endolysin from Cp-1, a Phage Infecting Streptococcus Pneumoniae Authors: Monterroso, B. / Albert, A. / Martinez-Ripoll, M. / Garcia, P. / Garcia, J.L. / Menendez, M. / Hermoso, J.A. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j8f.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j8f.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 2j8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/2j8f ftp://data.pdbj.org/pub/pdb/validation_reports/j8/2j8f | HTTPS FTP |
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-Related structure data
Related structure data | 2ixuC 2ixvC 2j8gC 1h09S 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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 39220.410 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-339 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTERIOPHAGE CP-1 (virus) / Production host: ESCHERICHIA COLI DH1 (bacteria) / References: UniProt: P15057, lysozyme |
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#2: Polysaccharide |
-Non-polymers , 4 types, 337 molecules
#3: Chemical | #4: Chemical | ChemComp-DGL / | #5: Chemical | ChemComp-FMT / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.29 % / Description: NONE |
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Crystal grow | pH: 6 / Details: pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→64.55 Å / Num. obs: 47836 / % possible obs: 96.3 % / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 1.84→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 0.9 / % possible all: 81.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H09 Resolution: 1.84→64.55 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.017 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→64.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.89 Å / Total num. of bins used: 20 /
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