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Yorodumi- PDB-4aqo: CRYSTAL STRUCTURE OF THE CALCIUM BOUND PKD-like DOMAIN OF COLLAGE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aqo | ||||||
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Title | CRYSTAL STRUCTURE OF THE CALCIUM BOUND PKD-like DOMAIN OF COLLAGENASE G FROM CLOSTRIDIUM HISTOLYTICUM AT 0.99 ANGSTROM RESOLUTION. | ||||||
Components | COLLAGENASE | ||||||
Keywords | HYDROLASE / PKD-LIKE DOMAIN / COLLAGENOLYSIS / COLLAGEN / RECRUITMENT / TWO- TIERED BETA BARREL | ||||||
Function / homology | Function and homology information 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 | CLOSTRIDIUM HISTOLYTICUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å | ||||||
Authors | Eckhard, U. / Brandstetter, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aqo.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aqo.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 4aqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aqo_validation.pdf.gz | 412.4 KB | Display | wwPDB validaton report |
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Full document | 4aqo_full_validation.pdf.gz | 413.1 KB | Display | |
Data in XML | 4aqo_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 4aqo_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/4aqo ftp://data.pdbj.org/pub/pdb/validation_reports/aq/4aqo | HTTPS FTP |
-Related structure data
Related structure data | 4ar1C 4ar8C 4ar9C 4areC 4arfC 2y72S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9672.577 Da / Num. of mol.: 1 / Fragment: PKD-LIKE DOMAIN, RESIDUES 792-880 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM HISTOLYTICUM (bacteria) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X721, microbial collagenase |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.4 % / Description: NONE |
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Crystal grow | Details: 0.1 M POTASSIUM THIOCYANATE, 30% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000 |
-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: 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: 0.99→35.4 Å / Num. obs: 32608 / % possible obs: 91.8 % / Observed criterion σ(I): 12.1 / Redundancy: 3.4 % / Biso Wilson estimate: 5.4 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 0.99→1.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 12.1 / % possible all: 77.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y72 Resolution: 0.99→35.45 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.485 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.025 / 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: 8.086 Å2
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Refinement step | Cycle: LAST / Resolution: 0.99→35.45 Å
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