[English] 日本語
Yorodumi- PDB-2ixu: Crystal structure of the modular Cpl-1 endolysin complexed with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ixu | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (wild-type endolysin) | |||||||||||||||
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: 2.28 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 |
| |||||||||||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ixu.cif.gz | 89 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ixu.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ixu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ixu_validation.pdf.gz | 847.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ixu_full_validation.pdf.gz | 851.3 KB | Display | |
Data in XML | 2ixu_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 2ixu_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/2ixu ftp://data.pdbj.org/pub/pdb/validation_reports/ix/2ixu | HTTPS FTP |
-Related structure data
Related structure data | 2ixvC 2j8fC 2j8gC 1h09S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 39221.398 Da / Num. of mol.: 1 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 |
---|---|
#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, 175 molecules
#3: Chemical | ChemComp-FMT / |
---|---|
#4: Chemical | ChemComp-ALA / |
#5: Chemical | ChemComp-ZGL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.21 % / Description: NONE |
---|---|
Crystal grow | pH: 6 / Details: pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 14, 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: 2.28→25.86 Å / Num. obs: 32678 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 9.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.26→2.41 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 99.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H09 Resolution: 2.28→25.32 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.773 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→25.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.28→2.339 Å / Total num. of bins used: 20 /
|