[English] 日本語
Yorodumi- PDB-4arf: CRYSTAL STRUCTURE OF THE PEPTIDASE DOMAIN OF COLLAGENASE H FROM C... -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 4arf | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Title | CRYSTAL STRUCTURE OF THE PEPTIDASE DOMAIN OF COLLAGENASE H FROM CLOSTRIDIUM HISTOLYTICUM IN COMPLEX WITH THE PEPTIDIC INHIBITOR ISOAMYLPHOSPHONYL-GLY-PRO-ALA AT 1.77 ANGSTROM RESOLUTION. | ||||||||||||
Components |
| ||||||||||||
Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / COLLAGENOLYSIS / HYDROLYSE / METALLOPROTEASE / HEXXH | ||||||||||||
| Function / homology | Function and homology informationtripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / extracellular region / zinc ion binding Similarity search - Function | ||||||||||||
| Biological species | CLOSTRIDIUM HISTOLYTICUM (bacteria)SYNTHETIC CONSTRUCT (others) | ||||||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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. | ||||||||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 4arf.cif.gz | 183.6 KB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb4arf.ent.gz | 145.2 KB | Display | PDB format |
| PDBx/mmJSON format | 4arf.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/4arf ftp://data.pdbj.org/pub/pdb/validation_reports/ar/4arf | HTTPS FTP |
|---|
-Related structure data
| Related structure data | ![]() 4aqoC ![]() 4ar1C ![]() 4ar8C ![]() 4ar9C ![]() 4areC ![]() 2y3uS C: citing same article ( S: Starting model for refinement |
|---|---|
| Similar structure data |
-
Links
-
Assembly
| Deposited unit | ![]()
| |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ![]()
| |||||||||
| Unit cell |
| |||||||||
| Components on special symmetry positions |
|
-
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.) CLOSTRIDIUM HISTOLYTICUM (bacteria) / Production host: ![]() |
|---|---|
| #2: Protein/peptide | Mass: 391.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
| #3: Chemical | ChemComp-ZN / |
| #4: Chemical | ChemComp-CA / |
| #5: Water | ChemComp-HOH / |
| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
|---|
-
Sample preparation
| Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.37 % / Description: NONE |
|---|---|
| Crystal grow | pH: 7.25 / Details: 22.5% PEG3350, 0.15M SODIUM FORMATE, PH 7.25 |
-Data collection
| Diffraction | Mean temperature: 100 K |
|---|---|
| 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: 1.77→40 Å / Num. obs: 42481 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10 |
| Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 86.2 |
-
Processing
| Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 2Y3U Resolution: 1.77→40 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.339 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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: 25.437 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 1.77→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
|
Movie
Controller
About Yorodumi



CLOSTRIDIUM HISTOLYTICUM (bacteria)
X-RAY DIFFRACTION
Citation















PDBj




