+Open data
-Basic information
Entry | Database: PDB / ID: 3msf | ||||||
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Title | Crystal structure of Thermolysin in complex with Urea | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE / PROTEASE / Fragment soaking / METALLOPROTEASE / Metal-binding / Secreted / Zymogen / Urea / Fragment based lead discovery | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.09 Å | ||||||
Authors | Behnen, J. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Chemmedchem / Year: 2012 Title: Experimental and computational active site mapping as a starting point to fragment-based lead discovery. Authors: Behnen, J. / Koster, H. / Neudert, G. / Craan, T. / 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 | 3msf.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3msf.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 3msf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3msf_validation.pdf.gz | 450.2 KB | Display | wwPDB validaton report |
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Full document | 3msf_full_validation.pdf.gz | 453.7 KB | Display | |
Data in XML | 3msf_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 3msf_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/3msf ftp://data.pdbj.org/pub/pdb/validation_reports/ms/3msf | HTTPS FTP |
-Related structure data
Related structure data | 3ms3C 3msaC 3msnC 3n21C 3n4aC 3n9wC 3nn7C 3nx8C 3pczC 3prsC 3pvkC 3pwwC 2a7gS 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 A
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin |
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-Non-polymers , 5 types, 172 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-URE / | #5: Chemical | #6: 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: 2.32 Å3/Da / Density % sol: 46.95 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50 mM Tris/HCl, 50 % DMSO, 1.8 M CsCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 16, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→25 Å / Num. all: 19899 / Num. obs: 19899 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rsym value: 0.134 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.09→2.13 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 967 / Rsym value: 0.476 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2A7G Resolution: 2.09→10 Å / Num. parameters: 10446 / Num. restraintsaints: 10143 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 2238 / Occupancy sum non hydrogen: 2594.02 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.13 Å / Num. reflection obs: 18714 |