+Open data
-Basic information
Entry | Database: PDB / ID: 5lvd | ||||||
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Title | Thermolysin in complex with inhibitor (JC67) | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE / 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: 1.25 Å | ||||||
Authors | Krimmer, S.G. / Cramer, J. / Heine, A. / Klebe, G. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1' Pocket of Thermolysin. Authors: Krimmer, S.G. / Cramer, J. / Schiebel, J. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lvd.cif.gz | 208.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lvd.ent.gz | 168.1 KB | Display | PDB format |
PDBx/mmJSON format | 5lvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/5lvd ftp://data.pdbj.org/pub/pdb/validation_reports/lv/5lvd | HTTPS FTP |
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-Related structure data
Related structure data | 5m5fC 5m69C 5m9wC 5ma7C 8tlnS 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 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, 396 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-79F / ( | #7: 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: 2.35 Å3/Da / Density % sol: 47.66 % |
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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 DOUBLE CRYSTAL MONOCHROMATOR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013 |
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: 1.25→50 Å / Num. obs: 91830 / % possible obs: 99.9 % / Redundancy: 24.86 % / Rsym value: 0.066 / Net I/σ(I): 35.16 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 24.72 % / Rmerge(I) obs: 0.495 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8TLN Resolution: 1.25→38.243 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 8.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→38.243 Å
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Refine LS restraints |
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LS refinement shell |
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