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- PDB-6y6r: Crystal structure of MINDY1 T335D mutant -

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Basic information

Entry
Database: PDB / ID: 6y6r
TitleCrystal structure of MINDY1 T335D mutant
ComponentsUbiquitin carboxyl-terminal hydrolase MINDY-1
KeywordsHYDROLASE / CYSTEINE PROTEASE / ISOPEPTIDASE AND UBIQUITIN BINDING
Function / homology
Function and homology information


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
MINDY deubiquitinase / MINDY deubiquitinase domain / MINDY deubiquitinase
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase MINDY-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.32 Å
AuthorsAbdul Rehman, S.A. / Kulathu, Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_12016/6 United Kingdom
European Research Council (ERC)677623 United Kingdom
CitationJournal: Mol.Cell / Year: 2021
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
DepositionFeb 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / diffrn_source / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 3, 2021Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase MINDY-1


Theoretical massNumber of molelcules
Total (without water)32,0521
Polymers32,0521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.810, 99.810, 164.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase MINDY-1 / Deubiquitinating enzyme MINDY-1 / Protein FAM63A


Mass: 32052.201 Da / Num. of mol.: 1 / Mutation: T335D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MINDY1, FAM63A, KIAA1390 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N5J2, ubiquitinyl hydrolase 1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 6.38 Å3/Da / Density % sol: 80.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 0.8 M Potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 3.32→85.28 Å / Num. obs: 12828 / % possible obs: 99.4 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.03 / Rrim(I) all: 0.07 / Net I/σ(I): 13.2 / Num. measured all: 70094
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.32-3.584.61.1821156425110.7210.6071.3351.297.4
8.77-85.2850.02539377900.9990.0120.02850.399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JKN

5jkn


Resolution: 3.32→85.21 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 21.483 / SU ML: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.464 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 600 4.7 %RANDOM
Rwork0.1996 ---
obs0.2018 12210 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 346.61 Å2 / Biso mean: 150.707 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-6.93 Å20 Å20 Å2
2--6.93 Å20 Å2
3----13.87 Å2
Refinement stepCycle: final / Resolution: 3.32→85.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 0 0 1986
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132050
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171787
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.6282805
X-RAY DIFFRACTIONr_angle_other_deg1.2381.5614164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6955257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62525.20498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.42415312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.694153
X-RAY DIFFRACTIONr_chiral_restr0.0720.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022306
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02399
LS refinement shellResolution: 3.32→3.401 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.425 38 -
Rwork0.458 836 -
obs--95.21 %

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