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- PDB-6k6l: YGL082W-catalytic domain -

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Basic information

Entry
Database: PDB / ID: 6k6l
TitleYGL082W-catalytic domain
Componentspseudo deubiquitinase
KeywordsUNKNOWN FUNCTION / Pseudo Deubiquitinase
Function / homology
Function and homology information


cysteine-type carboxypeptidase activity / protein K48-linked deubiquitination / K48-linked deubiquitinase activity / cell periphery / cysteine-type deubiquitinase activity / nucleus / plasma membrane / cytoplasm
Similarity search - Function
MINDY deubiquitinase / MINDY deubiquitinase domain / MINDY deubiquitinase
Similarity search - Domain/homology
Uncharacterized protein YGL082W
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsLu, L.N. / Wang, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Sci China Chem / Year: 2019
Title: Inactivity of YGL082W in vitro due to impairment of conformational change in the catalytic center loop
Authors: Lu, L. / Guo, Y. / Wang, T. / Liang, L. / Zhao, S. / Wang, F. / Liu, L.
History
DepositionJun 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: pseudo deubiquitinase
B: pseudo deubiquitinase


Theoretical massNumber of molelcules
Total (without water)63,7852
Polymers63,7852
Non-polymers00
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-13 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.940, 70.640, 68.380
Angle α, β, γ (deg.)90.00, 102.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein pseudo deubiquitinase


Mass: 31892.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YGL082W / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53155
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 18% w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.77→66.75 Å / Num. obs: 54216 / % possible obs: 97.98 % / Redundancy: 6.8 % / Net I/σ(I): 13.9
Reflection shellResolution: 1.77→1.833 Å / Num. unique obs: 54191

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JKN

5jkn


Resolution: 1.77→66.75 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.828 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24111 2647 4.9 %RANDOM
Rwork0.18917 ---
obs0.19175 51556 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.682 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å2-0 Å20.29 Å2
2---0.52 Å2-0 Å2
3---2.31 Å2
Refinement stepCycle: 1 / Resolution: 1.77→66.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 0 372 4486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194239
X-RAY DIFFRACTIONr_bond_other_d0.0030.023776
X-RAY DIFFRACTIONr_angle_refined_deg2.1451.9485745
X-RAY DIFFRACTIONr_angle_other_deg1.23738787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6355519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38525.273220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30215712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7081520
X-RAY DIFFRACTIONr_chiral_restr0.1650.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024771
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02849
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_it3.5513.2222085
X-RAY DIFFRACTIONr_mcbond_other3.5373.222084
X-RAY DIFFRACTIONr_mcangle_it4.7464.8212601
X-RAY DIFFRACTIONr_mcangle_other4.7474.8232602
X-RAY DIFFRACTIONr_scbond_it4.9473.7682154
X-RAY DIFFRACTIONr_scbond_other4.9463.7692155
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1145.463145
X-RAY DIFFRACTIONr_long_range_B_refined9.48741.3835167
X-RAY DIFFRACTIONr_long_range_B_other9.46941.0545079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 178 -
Rwork0.259 3682 -
obs--94.72 %

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