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Open data
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Basic information
Entry | Database: PDB / ID: 6z49 | |||||||||
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Title | Crystal structure of deubiquitinase Mindy2 | |||||||||
![]() | Ubiquitin carboxyl-terminal hydrolase MINDY-2 | |||||||||
![]() | HYDROLASE / CYSTEINE PROTEASE / ISOPEPTIDASE AND UBIQUITIN BINDING | |||||||||
Function / homology | ![]() K11-linked polyubiquitin modification-dependent protein binding / K6-linked polyubiquitin modification-dependent protein binding / cysteine-type carboxypeptidase activity / K48-linked deubiquitinase activity / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / proteolysis / nucleoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Abdul Rehman, S.A. / Kulathu, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2. Authors: Abdul Rehman, S.A. / Armstrong, L.A. / Lange, S.M. / Kristariyanto, Y.A. / Grawert, T.W. / Knebel, A. / Svergun, D.I. / Kulathu, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.3 KB | Display | ![]() |
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PDB format | ![]() | 164 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tuvC ![]() 6txbC ![]() 6y6rC ![]() 6yjgC ![]() 6z7vC ![]() 6z90C ![]() 7npiC ![]() 5jknS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31200.455 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.47 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Bis-Tris pH 6.0, 0.2 M Magnesium chloride and 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07252 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.72 Å / Num. obs: 83541 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.028 / Rrim(I) all: 0.059 / Net I/σ(I): 13.9 / Num. measured all: 344672 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.673 / Num. unique obs: 4588 / CC1/2: 0.814 / Rpim(I) all: 0.376 / Rrim(I) all: 0.773 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JKN Resolution: 2→47.72 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.129 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 131.78 Å2 / Biso mean: 42.468 Å2 / Biso min: 22.28 Å2
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Refinement step | Cycle: final / Resolution: 2→47.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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