+Open data
-Basic information
Entry | Database: PDB / ID: 3f28 | ||||||
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Title | Thermolysin inhibition | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE / protein fragment complex / Calcium / Metal-binding / Metalloprotease / Protease / Secreted / Zinc / Zymogen | ||||||
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: 1.68 Å | ||||||
Authors | Englert, L. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Chemmedchem / Year: 2010 Title: Fragment-Based Lead Discovery: Screening and Optimizing Fragments for Thermolysin Inhibition. Authors: Englert, L. / Silber, K. / Steuber, H. / Brass, S. / Over, B. / Gerber, H.D. / Heine, A. / Diederich, W.E. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f28.cif.gz | 80.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f28.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 3f28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/3f28 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/3f28 | HTTPS FTP |
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-Related structure data
Related structure data | 3f2pC 3fcqC 1tmnS 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
#1: Protein | Mass: 34362.305 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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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-S7B / | #5: 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: 2.12 Å3/Da / Density % sol: 46.94 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50mMTris/HCl, 50%DMSO, 1.9MCsCl, 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: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2008 / Details: Double crystal monochromator |
Radiation | Monochromator: Double crystal monochromator KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→30 Å / Num. all: 37792 / Num. obs: 37792 / % possible obs: 99.8 % / Redundancy: 9.8 % / Rsym value: 0.063 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 1852 / Rsym value: 0.481 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1TMN Resolution: 1.68→10 Å / Num. parameters: 10406 / Num. restraintsaints: 10245 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2562 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→10 Å
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Refine LS restraints |
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