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Yorodumi- PDB-3de0: Proteinase K by LB nanotemplate method after the second step of h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3de0 | ||||||
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Title | Proteinase K by LB nanotemplate method after the second step of high X-Ray dose on ESRF ID23-1 beamline | ||||||
Components | Proteinase K | ||||||
Keywords | HYDROLASE / Alpha and beta proteins / Subtilases / proteinase K / Calcium / Metal-binding / Protease / Serine protease / Zymogen | ||||||
Function / homology | Function and homology information peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Engyodontium album (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Pechkova, E. / Tripathi, S.K. / Nicolini, C. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2009 Title: Radiation stability of proteinase K crystals grown by LB nanotemplate method Authors: Pechkova, E. / Tripathi, S. / Ravelli, R.B. / McSweeney, S. / Nicolini, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3de0.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3de0.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 3de0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/3de0 ftp://data.pdbj.org/pub/pdb/validation_reports/de/3de0 | HTTPS FTP |
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-Related structure data
Related structure data | 3d9qC 3ddzSC 3de1C 3de2C 3de3C 3de4C 3de5C 3de6C 3de7C 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
#1: Protein | Mass: 28930.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K |
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#2: Chemical | ChemComp-CA / |
#3: 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: 2.01 Å3/Da / Density % sol: 38.81 % / Mosaicity: 0.4 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20mg/ml of protein in 25mM HEPES, pH7.0, reservoir solution composed by 25mM HEPES and 400mM Na/K tartrate at pH7.0. Onto the siliconized glass cover slides were mixed 4 microL of protein ...Details: 20mg/ml of protein in 25mM HEPES, pH7.0, reservoir solution composed by 25mM HEPES and 400mM Na/K tartrate at pH7.0. Onto the siliconized glass cover slides were mixed 4 microL of protein solution with 4 microL of reservoir solution., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→56.344 Å / Num. obs: 17199 / % possible obs: 89.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 1.8 / Num. measured all: 12851 / Num. unique all: 2460 / Rsym value: 0.293 / % possible all: 89.3 |
-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 3DDZ Resolution: 1.9→34.83 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.883 / SU B: 2.87 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 5.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→34.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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