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- PDB-4ar8: Crystal structure of the peptidase domain of collagenase T from C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ar8 | ||||||
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Title | Crystal structure of the peptidase domain of collagenase T from Clostridium tetani complexed with the peptidic inhibitor isoamyl- phosphonyl-Gly-Pro-Ala at 2.05 angstrom resolution. | ||||||
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![]() | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() SYNTHETIC CONSTRUCT (others) | ||||||
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 | ![]() | 340 KB | Display | ![]() |
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PDB format | ![]() | 277.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4aqoC ![]() 4ar1C ![]() 4ar9C ![]() 4areC ![]() 4arfC ![]() 2y3uS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45750.816 Da / Num. of mol.: 2 / Fragment: PEPTIDASE DOMAIN, RESIDUES 340-730 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 391.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.78 % / Description: NONE |
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Crystal grow![]() | pH: 6.5 / Details: 25% PEG 3350, 0.1 M NACL, 0.1 M MES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.05→45.7 Å / Num. obs: 48639 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2Y3U Resolution: 2.05→45.75 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.714 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 31.109 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→45.75 Å
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Refine LS restraints |
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