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Open data
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Basic information
Entry | Database: PDB / ID: 6z90 | |||||||||
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Title | Crystal structure of MINDY1 mutant-P138A | |||||||||
![]() | Ubiquitin carboxyl-terminal hydrolase MINDY-1 | |||||||||
![]() | HYDROLASE / CYSTEINE PROTEASE / ISOPEPTIDASE AND UBIQUITIN BINDING | |||||||||
Function / homology | ![]() cysteine-type carboxypeptidase activity / K48-linked deubiquitinase activity / K48-linked polyubiquitin modification-dependent protein binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / 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 | ![]() | 64.1 KB | Display | ![]() |
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PDB format | ![]() | 45.2 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 ![]() 6z49C ![]() 6z7vC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 32012.182 Da / Num. of mol.: 1 / Mutation: P138A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.7 M sodium citrate tribasic dihydrate, 0.1 M BIS-TRIS propane pH 7.0 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 3.59→48.28 Å / Num. obs: 10152 / % possible obs: 99.9 % / Redundancy: 8.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.034 / Rrim(I) all: 0.1 / Net I/σ(I): 12.5 / Num. measured all: 86341 |
Reflection shell | Resolution: 3.59→3.93 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.037 / Num. unique obs: 2353 / CC1/2: 0.905 / Rpim(I) all: 0.368 / Rrim(I) all: 1.101 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JKN Resolution: 3.59→48 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.952 / SU B: 27.942 / SU ML: 0.363 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.805 / ESU R Free: 0.425 / 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: 329.16 Å2 / Biso mean: 169.231 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 3.59→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.59→3.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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