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- PDB-6yjg: Crystal structure of MINDY1 mutant-Y114F -

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Basic information

Entry
Database: PDB / ID: 6yjg
TitleCrystal structure of MINDY1 mutant-Y114F
ComponentsUbiquitin carboxyl-terminal hydrolase MINDY1
KeywordsHYDROLASE / CYSTEINE PROTEASE / ISOPEPTIDASE AND UBIQUITIN BINDING
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.28 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
DepositionApr 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 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 MINDY1


Theoretical massNumber of molelcules
Total (without water)32,0221
Polymers32,0221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13020 Å2
Unit cell
Length a, b, c (Å)102.160, 102.160, 162.714
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 MINDY1


Mass: 32022.217 Da / Num. of mol.: 1 / Mutation: Y114F
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: 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
Details: 0.1 M Tris-HCl pH 8.5, 1.5 M Ammonium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 3.28→72.24 Å / Num. obs: 13867 / % possible obs: 100 % / Redundancy: 27.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.282 / Rpim(I) all: 0.055 / Rrim(I) all: 0.288 / Net I/σ(I): 11.5 / Num. measured all: 378950 / Scaling rejects: 98
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
3.28-3.54271.7657498027810.9020.3431.7992.599.8
8.67-72.2422.90.0491977486510.010.0538.199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5jkn


Resolution: 3.28→72.21 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU B: 18.082 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.424 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 705 5.1 %RANDOM
Rwork0.205 ---
obs0.2071 13097 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 218.4 Å2 / Biso mean: 83.772 Å2 / Biso min: 53.56 Å2
Baniso -1Baniso -2Baniso -3
1-4.15 Å20 Å20 Å2
2--4.15 Å20 Å2
3----8.29 Å2
Refinement stepCycle: final / Resolution: 3.28→72.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 0 0 1984
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132034
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171783
X-RAY DIFFRACTIONr_angle_refined_deg2.041.6292781
X-RAY DIFFRACTIONr_angle_other_deg1.3291.5614139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.725257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73524.62493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.95815305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.612154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022288
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02404
LS refinement shellResolution: 3.28→3.365 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 38 -
Rwork0.388 961 -
all-999 -
obs--100 %

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