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- PDB-2y72: Crystal structure of the PKD Domain of Collagenase G from Clostri... -
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Open data
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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. | ||||||
![]() | COLLAGENASE | ||||||
![]() | HYDROLASE / POLYCYSTIC KIDNEY DISEASE DOMAIN / BETA BARREL / COLLAGEN RECOGNITION DOMAIN | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Eckhard, U. / Brandstetter, H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.5 KB | Display | ![]() |
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PDB format | ![]() | 73.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2y3uC ![]() 2y50C ![]() 2y6iC ![]() 2c26S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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Refine LS restraints |
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