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- PDB-6z49: Crystal structure of deubiquitinase Mindy2 -

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Basic information

Entry
Database: PDB / ID: 6z49
TitleCrystal structure of deubiquitinase Mindy2
ComponentsUbiquitin carboxyl-terminal hydrolase MINDY-2
KeywordsHYDROLASE / CYSTEINE PROTEASE / ISOPEPTIDASE AND UBIQUITIN BINDING
Function / homology
Function and homology information


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 / cell periphery / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / proteolysis / nucleoplasm
Similarity search - Function
MINDY deubiquitinase / MINDY deubiquitinase domain / MINDY deubiquitinase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Ubiquitin carboxyl-terminal hydrolase MINDY-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionMay 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 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-2
B: Ubiquitin carboxyl-terminal hydrolase MINDY-2
C: Ubiquitin carboxyl-terminal hydrolase MINDY-2
D: Ubiquitin carboxyl-terminal hydrolase MINDY-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,56315
Polymers124,8024
Non-polymers76111
Water2,054114
1
A: Ubiquitin carboxyl-terminal hydrolase MINDY-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3423
Polymers31,2001
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase MINDY-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6076
Polymers31,2001
Non-polymers4075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin carboxyl-terminal hydrolase MINDY-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2362
Polymers31,2001
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin carboxyl-terminal hydrolase MINDY-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3774
Polymers31,2001
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.115, 120.420, 78.378
Angle α, β, γ (deg.)90.000, 92.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ubiquitin carboxyl-terminal hydrolase MINDY-2 / Deubiquitinating enzyme MINDY-2 / Protein FAM63B


Mass: 31200.455 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MINDY2, FAM63B, KIAA1164 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NBR6, ubiquitinyl hydrolase 1
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07252 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07252 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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: 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 4169 5 %RANDOM
Rwork0.2153 ---
obs0.2172 79342 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.78 Å2 / Biso mean: 42.468 Å2 / Biso min: 22.28 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å20 Å2-1.81 Å2
2---2.06 Å20 Å2
3---4.43 Å2
Refinement stepCycle: final / Resolution: 2→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7794 0 41 114 7949
Biso mean--64.97 38.79 -
Num. residues----1007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138003
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177095
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.63210894
X-RAY DIFFRACTIONr_angle_other_deg1.2971.56516435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2645999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41524.864368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.855151259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8961515
X-RAY DIFFRACTIONr_chiral_restr0.0710.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021577
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 303 -
Rwork0.349 5855 -
all-6158 -
obs--99.77 %

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