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Yorodumi- 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. | ||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / COLLAGENOLYSIS / METALLOPROTEASE / PEPTIDASE / HYDROLASE | ||||||
| Function / homology | Function and homology informationmicrobial collagenase / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / extracellular region / zinc ion binding Similarity search - Function | ||||||
| Biological species | CLOSTRIDIUM TETANI (bacteria)SYNTHETIC CONSTRUCT (others) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Eckhard, U. / Brandstetter, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013Title: Structural Basis for Activity Regulation and Substrate Preference of Clostridial Collagenases G, H, and T. Authors: Eckhard, U. / Schonauer, E. / Brandstetter, H. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4ar8.cif.gz | 339.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb4ar8.ent.gz | 277.4 KB | Display | PDB format |
| PDBx/mmJSON format | 4ar8.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4ar8_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
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| Full document | 4ar8_full_validation.pdf.gz | 451.1 KB | Display | |
| Data in XML | 4ar8_validation.xml.gz | 31.1 KB | Display | |
| Data in CIF | 4ar8_validation.cif.gz | 44.2 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/4ar8 ftp://data.pdbj.org/pub/pdb/validation_reports/ar/4ar8 | HTTPS FTP |
-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.) CLOSTRIDIUM TETANI (bacteria) / Production host: ![]() #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 / | Has protein modification | Y | |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8856 |
| 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: 0.8856 Å / Relative weight: 1 |
| 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: MOLECULAR REPLACEMENTStarting 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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CLOSTRIDIUM TETANI (bacteria)
X-RAY DIFFRACTION
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