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Yorodumi- PDB-2ixv: Crystal structure of the modular Cpl-1 endolysin complexed with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ixv | ||||||||||||
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Title | Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (E94Q mutant) | ||||||||||||
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 | STREPTOCOCCUS PHAGE CP-1 (virus) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 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 (London) / 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 | 2ixv.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ixv.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ixv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/2ixv ftp://data.pdbj.org/pub/pdb/validation_reports/ix/2ixv | HTTPS FTP |
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-Related structure data
Related structure data | 2ixuC 2j8fC 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 39220.410 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PHAGE CP-1 (virus) / Production host: ESCHERICHIA COLI DH1 (bacteria) / References: UniProt: P15057, lysozyme |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 273 molecules
#3: Chemical | ChemComp-FMT / |
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#4: Chemical | ChemComp-ALA / |
#5: Chemical | ChemComp-DGN / |
#6: Water | ChemComp-HOH / |
-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: 3.14 Å3/Da / Density % sol: 60.84 % |
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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: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 30, 2003 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE MONOCROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→26.53 Å / Num. obs: 40900 / % possible obs: 99.4 % / Observed criterion σ(I): 1.5 / Redundancy: 4.3 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 1.96→2.08 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H09 Resolution: 1.96→26.53 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1734679.42 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.3827 Å2 / ksol: 0.402969 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.96→26.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.08 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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