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- PDB-3dvr: Proteinase K by LB nanotemplate method after the first step of hi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dvr | ||||||
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Title | Proteinase K by LB nanotemplate method after the first step of high X-Ray dose on ESRF ID14-2 beamline | ||||||
![]() | Proteinase K | ||||||
![]() | HYDROLASE / alpha and beta proteins / Calcium / Metal-binding / Protease / Serine protease / Zymogen | ||||||
Function / homology | ![]() peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pechkova, E. / Tripathi, S.K. / Nicolini, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.2 KB | Display | ![]() |
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PDB format | ![]() | 49.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.5 KB | Display | ![]() |
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Full document | ![]() | 432.8 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dnzC ![]() 3do0C ![]() 3do1C ![]() 3do2C ![]() 3dvqC ![]() 3dvsC ![]() 3dw1C ![]() 3dw3C ![]() 3dweC ![]() 3dznC ![]() 3dzpC ![]() 3dzrC ![]() 3e0aC ![]() 1ptkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.69 % / Mosaicity: 0.46 ° |
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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: ![]() ![]() ![]() |
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→56.614 Å / Num. obs: 99190 / % possible obs: 82.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.02→1.08 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.5 / Num. measured all: 8365 / Num. unique all: 5181 / Rsym value: 0.302 / % possible all: 30.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PTK Resolution: 1.02→56.61 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.887 / SU B: 0.363 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.037 / 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: 8.058 Å2 / Biso min: 2.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.02→56.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.025→1.051 Å / Total num. of bins used: 20
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