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Yorodumi- PDB-3do1: Thermolysin by Classical hanging drop method before high X-Ray do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3do1 | ||||||
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Title | Thermolysin by Classical hanging drop method before high X-Ray dose on ESRF ID14-2 beamline | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE / metalloproteinase / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.33 Å | ||||||
Authors | Pechkova, E. / Tripathi, S.K. / Nicolini, C. | ||||||
Citation | Journal: To be Published Title: Radiation damage in protein structural characterization by Synchrotron Radiation: State of the art and Nanotechnology-based perspective Authors: Pechkova, E. / Tripathi, S.K. / Nicolini, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3do1.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3do1.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 3do1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/3do1 ftp://data.pdbj.org/pub/pdb/validation_reports/do/3do1 | HTTPS FTP |
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-Related structure data
Related structure data | 3dnzC 3do0C 3do2C 3dvqC 3dvrC 3dvsC 3dw1C 3dw3C 3dweC 3dznC 3dzpC 3dzrC 3e0aC 1keiS 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
-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, 192 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-VAL / | #5: Chemical | ChemComp-LYS / | #6: 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: 2.31 Å3/Da / Density % sol: 46.79 % / Mosaicity: 0.58 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: DMSO, Ammonium sulfate, MES, hanging drop, 293K, pH6.0, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2007 / Details: Toroidal mirror |
Radiation | Monochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→80.13 Å / Num. obs: 64020 / % possible obs: 81 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.243 / Rsym value: 0.243 / Net I/σ(I): 3 |
Reflection shell | Resolution: 1.31→1.38 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.674 / Num. measured all: 3896 / Num. unique all: 2697 / Rsym value: 0.67384 / % possible all: 24.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KEI Resolution: 1.33→68.04 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.809 / SU B: 1.714 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.56 Å2 / Biso mean: 21.019 Å2 / Biso min: 12.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.33→68.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.33→1.365 Å / Total num. of bins used: 20 /
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