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- PDB-3de3: Proteinase K by Classical hanging drop method before high X-Ray d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3de3 | ||||||
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Title | Proteinase K by Classical hanging drop method before high X-Ray dose on ESRF ID23-1 beamline | ||||||
![]() | Proteinase K | ||||||
![]() | HYDROLASE / Alpha Beta protein / 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 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.2 KB | Display | ![]() |
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PDB format | ![]() | 50 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3d9qC ![]() 3ddzC ![]() 3de0C ![]() 3de1C ![]() 3de2C ![]() 3de4C ![]() 3de5C ![]() 3de6C ![]() 3de7C 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
#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: 2.03 Å3/Da / Density % sol: 39.3 % / Mosaicity: 0.31 ° |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 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: 1.426→56.465 Å / Num. obs: 34227 / % possible obs: 76.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.43→1.5 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 3.1 / Num. measured all: 1673 / Num. unique all: 1199 / Rsym value: 0.245 / % possible all: 19.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 8.288 Å2
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Refinement step | Cycle: LAST / Resolution: 1.43→43.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.426→1.463 Å / Total num. of bins used: 20
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