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Yorodumi- PDB-7z5u: Crystal structure of the peptidase domain of collagenase G from C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z5u | ||||||
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Title | Crystal structure of the peptidase domain of collagenase G from Clostridium histolyticum in complex with a hydroxamate-based inhibitor | ||||||
Components | Collagenase ColG | ||||||
Keywords | HYDROLASE / collagenase / hydroxamate / ColG / inhibitor / complex | ||||||
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 | Hathewaya histolytica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Schoenauer, E. / Brandstetter, H. | ||||||
Funding support | Austria, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Discovery and Characterization of Synthesized and FDA-Approved Inhibitors of Clostridial and Bacillary Collagenases. Authors: Alhayek, A. / Abdelsamie, A.S. / Schonauer, E. / Camberlein, V. / Hutterer, E. / Posselt, G. / Serwanja, J. / Blochl, C. / Huber, C.G. / Haupenthal, J. / Brandstetter, H. / Wessler, S. / Hirsch, A.K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z5u.cif.gz | 290.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z5u.ent.gz | 195.3 KB | Display | PDB format |
PDBx/mmJSON format | 7z5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z5u_validation.pdf.gz | 756.7 KB | Display | wwPDB validaton report |
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Full document | 7z5u_full_validation.pdf.gz | 757.7 KB | Display | |
Data in XML | 7z5u_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 7z5u_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/7z5u ftp://data.pdbj.org/pub/pdb/validation_reports/z5/7z5u | HTTPS FTP |
-Related structure data
Related structure data | 7zbvC 2y6iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47885.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hathewaya histolytica (bacteria) / Gene: colG / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X721, microbial collagenase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-IFW / ( |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Tris-Bicine pH 8.5,pentaethylene glycol, diethylene glycol, triethylene glycol,tetraethylene glycol, PEG 20,000 and PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2021 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→42.46 Å / Num. obs: 38367 / % possible obs: 90.52 % / Redundancy: 1.9 % / Biso Wilson estimate: 23.35 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.09 |
Reflection shell | Resolution: 1.8→1.86 Å / Num. unique obs: 3832 / CC1/2: 0.773 / % possible all: 91.91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2y6i Resolution: 1.8→42.46 Å / SU ML: 0.1692 / Cross valid method: FREE R-VALUE / Phase error: 20.4106 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.46 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 29.0799765164 Å / Origin y: 0.641578980356 Å / Origin z: 6.93304384311 Å
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Refinement TLS group | Selection details: all |