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Yorodumi- PDB-3jqx: Crystal structure of Clostridium histolyticum colH collagenase co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jqx | ||||||
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Title | Crystal structure of Clostridium histolyticum colH collagenase collagen binding domain 3 at 2.2 Angstrom resolution in the presence of calcium and cadmium | ||||||
Components | ColH protein | ||||||
Keywords | CELL ADHESION / beta barrel / dual calcium-binding motif / Collagen | ||||||
Function / homology | Function and homology information tripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Clostridium histolyticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Sakon, J. / Philominathan, S.T.L. / Bauer, R. / Matsushita, O. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2013 Title: Structural Comparison of ColH and ColG Collagen-Binding Domains from Clostridium histolyticum. Authors: Bauer, R. / Wilson, J.J. / Philominathan, S.T. / Davis, D. / Matsushita, O. / Sakon, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jqx.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jqx.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 3jqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jqx_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 3jqx_full_validation.pdf.gz | 451 KB | Display | |
Data in XML | 3jqx_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 3jqx_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/3jqx ftp://data.pdbj.org/pub/pdb/validation_reports/jq/3jqx | HTTPS FTP |
-Related structure data
Related structure data | 3jqwC 4hpkC 2o8oS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13412.737 Da / Num. of mol.: 3 / Fragment: collagen binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium histolyticum (bacteria) / Gene: colH / Production host: Escherichia coli (E. coli) / References: UniProt: Q46085, microbial collagenase #2: Chemical | #3: Chemical | ChemComp-CD / #4: Water | ChemComp-HOH / | |
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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: 2.37 Å3/Da / Density % sol: 48.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: sodium acetate, CdSO4,CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 18873 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.9 % / Rsym value: 0.12 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.2→2.5 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1431 / Rsym value: 0.54 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2o8o ColG-3b collagen binding domain Resolution: 2.2→28.68 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.905 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.309 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→28.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.196→2.253 Å / Total num. of bins used: 20
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