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- PDB-4are: Crystal structure of the collagenase Unit of collagenase G from C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4are | ||||||
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Title | Crystal structure of the collagenase Unit of collagenase G from Clostridium histolyticum at 2.19 angstrom resolution. | ||||||
![]() | COLLAGENASE G | ||||||
![]() | HYDROLASE / COLLAGEN / PEPTIDASE / COLLAGENOLYSIS / METALLOPROTEASE | ||||||
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: Structural Basis for Activity Regulation and Substrate Preference of Clostridial Collagenases G, H, and T. Authors: Eckhard, U. / Schonauer, E. / Brandstetter, H. #1: ![]() Title: Structure of Collagenase G Reveals a Chew-and- Digest Mechanism of Bacterial Collagenolysis. Authors: Eckhard, U. / Schoenauer, E. / Nuess, D. / 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 | ![]() | 301.5 KB | Display | ![]() |
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PDB format | ![]() | 244.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 658.6 KB | Display | ![]() |
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Full document | ![]() | 666.9 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 41.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aqoC ![]() 4ar1C ![]() 4ar8C ![]() 4ar9C ![]() 4arfC ![]() 2y3uS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 79477.461 Da / Num. of mol.: 1 / Fragment: COLLAGENASE UNIT, RESIDUES 119-790 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 273 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-P6G / |
#4: Chemical | ChemComp-FLC / |
#5: Chemical | ChemComp-TRS / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | DIFFERENT STRAIN USED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.78 % / Description: NONE |
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Crystal grow | pH: 8.25 / Details: 22.5% PEG 3350, 0.15M TRISODIUMCITRATE PH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→69.5 Å / Num. obs: 56974 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.19→2.31 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y3U Resolution: 2.19→69.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 17.625 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.615 / ESU R Free: 0.176 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.029 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→69.5 Å
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Refine LS restraints |
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