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Yorodumi- PDB-4cvd: Crystal structure of the central repeat of cell wall binding modu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cvd | ||||||
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Title | Crystal structure of the central repeat of cell wall binding module of Cpl7 | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / STREPTOCOCCUS PNEUMONIAE | ||||||
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 Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PHAGE CP-7 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.666 Å | ||||||
Authors | Silva-Martin, N. / Uson, I. / Rodriguez, D.D. / Hermoso, J.A. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Deciphering how Cpl-7 cell wall-binding repeats recognize the bacterial peptidoglycan. Authors: Bustamante, N. / Iglesias-Bexiga, M. / Bernardo-Garcia, N. / Silva-Martin, N. / Garcia, G. / Campanero-Rhodes, M.A. / Garcia, E. / Uson, I. / Buey, R.M. / Garcia, P. / Hermoso, J.A. / Bruix, M. / Menendez, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cvd.cif.gz | 19.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cvd.ent.gz | 12.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/4cvd ftp://data.pdbj.org/pub/pdb/validation_reports/cv/4cvd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5263.677 Da / Num. of mol.: 1 Fragment: CENTRAL REPEAT OF CELL WALL BINDING MODULE, RESIDUES 205-252 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PHAGE CP-7 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P19385, lysozyme |
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#2: 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: 2.34 Å3/Da / Density % sol: 47.4 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.3 M TRI-SODIUM CITRATE, HEGA-8 AS ADITIVE, VAPOR DIFFUSION, HANGING DROP, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 23, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→28.54 Å / Num. obs: 4935 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Biso Wilson estimate: 12.17 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.3 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: NONE Resolution: 1.666→25.2 Å / SU ML: 0.18 / σ(F): 1.54 / Phase error: 19.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 11 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.666→25.2 Å
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Refine LS restraints |
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LS refinement shell |
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