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Yorodumi- PDB-2y72: Crystal structure of the PKD Domain of Collagenase G from Clostri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y72 | ||||||
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Title | Crystal structure of the PKD Domain of Collagenase G from Clostridium Histolyticum at 1.18 Angstrom Resolution. | ||||||
Components | COLLAGENASE | ||||||
Keywords | HYDROLASE / POLYCYSTIC KIDNEY DISEASE DOMAIN / BETA BARREL / COLLAGEN RECOGNITION DOMAIN | ||||||
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: 1.18 Å | ||||||
Authors | Eckhard, U. / Brandstetter, H. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2011 Title: Structure of Collagenase G Reveals a Chew-and -Digest Mechanism of Bacterial Collagenolysis Authors: Eckhard, U. / Schoenauer, E. / Nuess, D. / Brandstetter, H. #1: Journal: Biol.Chem / Year: 2011 Title: Polycystic Kidney Disease-Like Domains of Clostridial Collagenases and Their Role in Collagen Recruitment. Authors: Eckhard, U. / Brandstetter, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y72.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y72.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 2y72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y72_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 2y72_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 2y72_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 2y72_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/2y72 ftp://data.pdbj.org/pub/pdb/validation_reports/y7/2y72 | HTTPS FTP |
-Related structure data
Related structure data | 2y3uC 2y50C 2y6iC 2c26S C: citing same article (ref.) S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 8946.764 Da / Num. of mol.: 2 Fragment: POLYCYSTIC KIDNEY DISEASE (PKD) DOMAIN, RESIDUES 799-880 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM HISTOLYTICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X721, microbial collagenase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.74 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 2.5M C3H2O4NA2, 10MM CACL2, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98793 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 12, 2010 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98793 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→40.51 Å / Num. obs: 56646 / % possible obs: 96.4 % / Observed criterion σ(I): 3.2 / Redundancy: 6 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.18→1.24 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.2 / % possible all: 78.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C26 Resolution: 1.18→44.94 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.108 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.061 Å2
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Refinement step | Cycle: LAST / Resolution: 1.18→44.94 Å
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