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- PDB-9ewp: Crystal structure of yeast E2 Ubiquitin-conjugating enzyme Ubc6 U... -

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Basic information

Entry
Database: PDB / ID: 9ewp
TitleCrystal structure of yeast E2 Ubiquitin-conjugating enzyme Ubc6 UBC domain
ComponentsUbiquitin-conjugating enzyme E2 6
KeywordsTRANSFERASE / Ubiquitin / Endoplasmic Reticulum / non-canonical ubiquitination
Function / homology: / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.21 Å
AuthorsSwarnkar, A. / Stein, A.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)677770European Union
German Research Foundation (DFG)SFB1190 Germany
CitationJournal: Embo J. / Year: 2024
Title: Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes.
Authors: Swarnkar, A. / Leidner, F. / Rout, A.K. / Ainatzi, S. / Schmidt, C.C. / Becker, S. / Urlaub, H. / Griesinger, C. / Grubmuller, H. / Stein, A.
History
DepositionApr 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 25, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,13513
Polymers20,3471
Non-polymers78812
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.139, 44.169, 97.578
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ubiquitin-conjugating enzyme E2 6 / E2 ubiquitin-conjugating enzyme 6 / Ubiquitin carrier protein UBC6 / Ubiquitin-protein ligase UBC6


Mass: 20347.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBC6, GI527_G0001907 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8H8ULW7, E2 ubiquitin-conjugating enzyme

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Non-polymers , 5 types, 253 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG smear, ethylene glycol, ammonium sulphate, cadmium chloride hydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→40.24 Å / Num. obs: 109888 / % possible obs: 99.55 % / Redundancy: 12.3 % / Biso Wilson estimate: 15.16 Å2 / CC1/2: 0.999 / Net I/σ(I): 25.47
Reflection shellResolution: 1.21→1.253 Å / Num. unique obs: 5615 / CC1/2: 0.876

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.21→40.24 Å / SU ML: 0.2057 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.3534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1557 5474 5.01 %
Rwork0.1346 103753 -
obs0.1356 109227 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.95 Å2
Refinement stepCycle: LAST / Resolution: 1.21→40.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 21 241 1651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01891451
X-RAY DIFFRACTIONf_angle_d1.61211973
X-RAY DIFFRACTIONf_chiral_restr0.102213
X-RAY DIFFRACTIONf_plane_restr0.0165255
X-RAY DIFFRACTIONf_dihedral_angle_d5.6424195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.221.08341580.97012958X-RAY DIFFRACTION84.35
1.22-1.240.72521800.68963417X-RAY DIFFRACTION97.85
1.24-1.250.32651790.42113382X-RAY DIFFRACTION97.8
1.25-1.270.29421830.28313506X-RAY DIFFRACTION98.87
1.27-1.280.23251830.23443418X-RAY DIFFRACTION99.28
1.28-1.30.26571820.23673484X-RAY DIFFRACTION99.27
1.3-1.320.29021820.25513410X-RAY DIFFRACTION99.72
1.32-1.340.33251870.29073549X-RAY DIFFRACTION99.47
1.34-1.360.33051780.24543433X-RAY DIFFRACTION99.75
1.36-1.380.20051870.20963510X-RAY DIFFRACTION99.81
1.38-1.410.15311870.17893467X-RAY DIFFRACTION99.86
1.41-1.430.16711840.14173495X-RAY DIFFRACTION99.7
1.43-1.460.16071850.11843470X-RAY DIFFRACTION100
1.46-1.490.14411820.10653486X-RAY DIFFRACTION100
1.49-1.520.13641840.10893465X-RAY DIFFRACTION99.95
1.52-1.560.1261820.10943490X-RAY DIFFRACTION100
1.56-1.60.14331840.11583510X-RAY DIFFRACTION99.95
1.6-1.640.17281820.11773468X-RAY DIFFRACTION99.95
1.64-1.690.14751840.11343497X-RAY DIFFRACTION100
1.69-1.740.13091810.09933465X-RAY DIFFRACTION100
1.74-1.810.12411880.10393516X-RAY DIFFRACTION100
1.81-1.880.1441860.10643479X-RAY DIFFRACTION100
1.88-1.960.13141850.10573474X-RAY DIFFRACTION100
1.96-2.070.11821830.10463509X-RAY DIFFRACTION100
2.07-2.20.1441860.10613474X-RAY DIFFRACTION100
2.2-2.370.1241860.10633491X-RAY DIFFRACTION100
2.37-2.60.11641780.10983471X-RAY DIFFRACTION100
2.6-2.980.12511870.12333497X-RAY DIFFRACTION100
2.98-3.760.14921810.13043481X-RAY DIFFRACTION100
3.76-40.240.17661800.15623481X-RAY DIFFRACTION99.51

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