+Open data
-Basic information
Entry | Database: PDB / ID: 3msa | ||||||
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Title | Crystal structure of Thermolysin in complex with 3-Bromophenol | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE / PROTEASE / Fragment soaking / METALLOPROTEASE / Metal-binding / Secreted / Zymogen / 3-Bromophenol / 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.66 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 | 3msa.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3msa.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 3msa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3msa_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 3msa_full_validation.pdf.gz | 463 KB | Display | |
Data in XML | 3msa_validation.xml.gz | 16 KB | Display | |
Data in CIF | 3msa_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/3msa ftp://data.pdbj.org/pub/pdb/validation_reports/ms/3msa | HTTPS FTP |
-Related structure data
Related structure data | 3ms3C 3msfC 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 , 6 types, 229 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-CA / #5: Chemical | #6: Chemical | ChemComp-IPA / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.53 % |
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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 CsCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-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: Feb 16, 2008 / Details: silicon |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→25 Å / Num. all: 36281 / Num. obs: 36281 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rsym value: 0.083 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 1846 / Rsym value: 0.451 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2A7G Resolution: 1.66→10 Å / Num. parameters: 10796 / Num. restraintsaints: 10319 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 2251 / Occupancy sum non hydrogen: 2660.12 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.69 Å / Num. reflection obs: 36281 |