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- PDB-4ar1: Crystal Structure of the Peptidase Domain of Collagenase H from C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ar1 | ||||||
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Title | Crystal Structure of the Peptidase Domain of Collagenase H from Clostridium histolyticum at 2.01 Angstrom resolution. | ||||||
![]() | COLH PROTEIN | ||||||
![]() | HYDROLASE / COLLAGEN / COLLAGENOLYSIS / PEPTIDASE M9 / BACTERIAL PEPTIDASE | ||||||
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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.9 KB | Display | ![]() |
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PDB format | ![]() | 137.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.8 KB | Display | ![]() |
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Full document | ![]() | 426.3 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aqoC ![]() 4ar8C ![]() 4ar9C ![]() 4areC ![]() 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 on special symmetry positions |
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Components
#1: Protein | Mass: 45876.820 Da / Num. of mol.: 1 / Fragment: PEPTIDASE DOMAIN, RESIDUES 331-721 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Sequence details | THREE SEQUENCE CONFLICTS ARISE FROM A DIFFERENT STRAIN USED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.31 % / Description: NONE |
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Crystal grow | pH: 7.25 / Details: 22.5% PEG3350 AND 0.15M SODIUM FORMATE, PH 7.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→46.33 Å / Num. obs: 29831 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.01→2.12 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.76 / 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: 2.01→46.33 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.684 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R Free: 0.174 / 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: 26.759 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→46.33 Å
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Refine LS restraints |
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