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- PDB-5jkn: Crystal structure of deubiquitinase MINDY-1 -

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Basic information

Entry
Database: PDB / ID: 5jkn
TitleCrystal structure of deubiquitinase MINDY-1
ComponentsProtein FAM63A
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
: / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Ubiquitin carboxyl-terminal hydrolase MINDY-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAbdul Rehman, S.A. / Kulathu, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Mol.Cell / Year: 2016
Title: MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes.
Authors: Abdul Rehman, S.A. / Kristariyanto, Y.A. / Choi, S.Y. / Nkosi, P.J. / Weidlich, S. / Labib, K. / Hofmann, K. / Kulathu, Y.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.4May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein FAM63A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4404
Polymers32,0381
Non-polymers4023
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-30 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.671, 99.671, 165.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Protein FAM63A


Mass: 32038.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM63A, KIAA1390 / Plasmid: pGEX6P1 / Production host: Escherichia coli / Strain (production host): BL21(DE3) / References: UniProt: Q8N5J2
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg

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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: 7.5 / Details: 100mM Hepes-Na pH 7.5, 200mM NaCl and 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93927 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 3→99.67 Å / Num. obs: 17325 / % possible obs: 99.8 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.4
Reflection shellResolution: 3→3.18 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.866 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Partial model obatined from experimental phasing

Resolution: 3→99.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.907 / SU B: 15.275 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24231 856 5 %RANDOM
Rwork0.19686 ---
obs0.19907 16430 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 118.197 Å2
Baniso -1Baniso -2Baniso -3
1-5.56 Å20 Å20 Å2
2--5.56 Å20 Å2
3----11.12 Å2
Refinement stepCycle: LAST / Resolution: 3→99.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 13 0 2015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192072
X-RAY DIFFRACTIONr_bond_other_d0.0010.021907
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9482826
X-RAY DIFFRACTIONr_angle_other_deg0.88234392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2455256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91325.47495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24515325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.037154
X-RAY DIFFRACTIONr_chiral_restr0.0680.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.77911.7311024
X-RAY DIFFRACTIONr_mcbond_other5.75911.7271023
X-RAY DIFFRACTIONr_mcangle_it9.33417.5751277
X-RAY DIFFRACTIONr_mcangle_other9.3317.5811278
X-RAY DIFFRACTIONr_scbond_it5.57212.2781048
X-RAY DIFFRACTIONr_scbond_other5.56712.2851044
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.20718.2191543
X-RAY DIFFRACTIONr_long_range_B_refined12.82692.8732199
X-RAY DIFFRACTIONr_long_range_B_other12.82492.9012200
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 62 -
Rwork0.384 1169 -
obs--99.92 %

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