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Yorodumi- PDB-3dvq: Proteinase K by LB nanotemplate method before high X-Ray dose on ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dvq | ||||||
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Title | Proteinase K by LB nanotemplate method before high X-Ray dose on ESRF ID14-2 beamline | ||||||
Components | Proteinase K | ||||||
Keywords | HYDROLASE / alpha and beta proteins / Calcium / Metal-binding / Protease / Serine protease / Zymogen | ||||||
Function / homology | Function and homology information peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Tritirachium album (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 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 | 3dvq.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dvq.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 3dvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/3dvq ftp://data.pdbj.org/pub/pdb/validation_reports/dv/3dvq | HTTPS FTP |
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-Related structure data
Related structure data | 3dnzC 3do0C 3do1C 3do2C 3dvrC 3dvsC 3dw1C 3dw3C 3dweC 3dznC 3dzpC 3dzrC 3e0aC 1ptkS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28930.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tritirachium 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: 2.04 Å3/Da / Density % sol: 39.62 % / Mosaicity: 0.43 ° |
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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 microlitres of ...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 microlitres of protein solution with 4 microlitres of reservoir solution., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2007 / Details: Toroidal mirror |
Radiation | Monochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→56.568 Å / Num. obs: 99486 / % possible obs: 83 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.02→1.08 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 3.9 / Num. measured all: 8241 / Num. unique all: 5123 / Rsym value: 0.194 / % possible all: 30.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PTK Resolution: 1.02→48.06 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.877 / SU B: 0.349 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.038 / 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: 200 Å2 / Biso mean: 6.588 Å2 / Biso min: 2.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.02→48.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.02→1.05 Å / Total num. of bins used: 20
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