+Open data
-Basic information
Entry | Database: PDB / ID: 5dpf | ||||||
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Title | Thermolysin in complex with inhibitor. | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE / PROTEASE / METALLOPROTEASE / HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus thermoproteolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Krimmer, S.G. / Heine, A. / Klebe, G. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J. Comput. Aided Mol. Des. / Year: 2015 Title: Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data. Authors: Krimmer, S.G. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dpf.cif.gz | 206.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dpf.ent.gz | 166 KB | Display | PDB format |
PDBx/mmJSON format | 5dpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/5dpf ftp://data.pdbj.org/pub/pdb/validation_reports/dp/5dpf | HTTPS FTP |
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-Related structure data
Related structure data | 5dpeC 8tlnS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Fragment: UNP residues 233-548 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin |
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-Non-polymers , 6 types, 387 molecules
#2: Chemical | ChemComp-5H9 / | ||||||
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#3: Chemical | ChemComp-ZN / | ||||||
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-DMS / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.42 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 MM TRIS/HCL, 1.9 M CSCL, 50% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2012 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→50 Å / Num. obs: 56522 / % possible obs: 99.5 % / Redundancy: 9.2 % / Rsym value: 0.073 / Net I/σ(I): 29.33 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 6.38 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8TLN Resolution: 1.47→40.161 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→40.161 Å
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Refine LS restraints |
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LS refinement shell |
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