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- PDB-6z90: Crystal structure of MINDY1 mutant-P138A -

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Basic information

Entry
Database: PDB / ID: 6z90
TitleCrystal structure of MINDY1 mutant-P138A
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 / Resolution: 3.59 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
DepositionJun 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 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 / 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
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 / pdbx_initial_refinement_model

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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)32,0121
Polymers32,0121
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 area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.649, 98.649, 166.073
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: 32012.182 Da / Num. of mol.: 1 / Mutation: P138A
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

Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JKN

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 525 5.2 %RANDOM
Rwork0.2117 ---
obs0.2139 9595 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 329.16 Å2 / Biso mean: 169.231 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-8.73 Å20 Å20 Å2
2--8.73 Å20 Å2
3----17.46 Å2
Refinement stepCycle: final / Resolution: 3.59→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 0 0 1946
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131996
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171717
X-RAY DIFFRACTIONr_angle_refined_deg1.671.6282736
X-RAY DIFFRACTIONr_angle_other_deg1.21.5563982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1265254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.51325.16193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.25215286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.753153
X-RAY DIFFRACTIONr_chiral_restr0.0630.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022261
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02392
LS refinement shellResolution: 3.59→3.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 41 -
Rwork0.493 695 -
all-736 -
obs--99.73 %

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