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- PDB-4jgu: Crystal structure of Clostridium histolyticum ColH collagenase po... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jgu | ||||||
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Title | Crystal structure of Clostridium histolyticum ColH collagenase polycystic kidney-disease-like domain 2b at 1.4 Angstrom resolution in the presence of calcium | ||||||
![]() | ColH protein | ||||||
![]() | METAL BINDING PROTEIN / IG-like fold / beta-sandwich / calcium binding protein | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Bauer, R. / Matsushita, O. / Sakon, J. | ||||||
![]() | ![]() Title: Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH. Authors: Bauer, R. / Janowska, K. / Taylor, K. / Jordan, B. / Gann, S. / Janowski, T. / Latimer, E.C. / Matsushita, O. / Sakon, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.3 KB | Display | ![]() |
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PDB format | ![]() | 72.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.3 KB | Display | ![]() |
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Full document | ![]() | 430.3 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jrwC ![]() 4tn9C ![]() 4u6tC ![]() 4u7kC ![]() 3jqu 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: 10600.848 Da / Num. of mol.: 2 / Fragment: PKD-like domain, UNP residues 806-900 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 35% (w/v) PEG 5000, 0.2M ammonium sulfate, 0.1M MES pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 31, 2010 | ||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.42→22.19 Å / Num. all: 37914 / Num. obs: 36663 / % possible obs: 96.7 % / Redundancy: 3.5 % / Rsym value: 0.039 / Net I/σ(I): 33.1 | ||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3JQU ![]() 3jqu Resolution: 1.42→22.19 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.633 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.064 / 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: 14.121 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→22.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.418→1.455 Å / Total num. of bins used: 20
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