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- PDB-7yw1: crystal structure of UBE2O -

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Basic information

Entry
Database: PDB / ID: 7yw1
Titlecrystal structure of UBE2O
Components(E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
KeywordsCYTOSOLIC PROTEIN / UBE2O
Function / homologyUBE2O, SH3-B domain / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / ubiquitin conjugating enzyme activity / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
Function and homology information
Biological speciesTrametes pubescens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsFu, Z. / Zhu, W. / Huang, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Structural insights into the biochemical mechanism of the E2/E3 hybrid enzyme UBE2O.
Authors: Huang, H. / Zhu, W. / Huang, B. / Fu, Z. / Xiong, Y. / Cao, D. / Ye, Y. / Chang, Q. / Li, W. / Li, L. / Zhou, H. / Niu, X. / Zhang, W.
History
DepositionAug 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
B: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O


Theoretical massNumber of molelcules
Total (without water)205,8862
Polymers205,8862
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.320, 132.529, 155.036
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O


Mass: 102942.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes pubescens (fungus) / Gene: TRAPUB_10883 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1M2VY70
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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / Details: PEG MME 5000, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97913697371156 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913697371156 Å / Relative weight: 1
ReflectionResolution: 3.27→100.74 Å / Num. obs: 28617 / % possible obs: 92 % / Redundancy: 12.8 % / CC1/2: 0.996 / Net I/σ(I): 9.5
Reflection shellResolution: 3.27→3.56 Å / Num. unique obs: 1431 / CC1/2: 0.604

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
PHENIXphasing
STARANISOdata scaling
PDB_EXTRACTdata extraction
PROCORdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 prediction

Resolution: 3.27→54.04 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.3002 --
Rwork0.2495 --
obs-28589 76.62 %
Refinement stepCycle: LAST / Resolution: 3.27→54.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10032 0 0 0 10032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001610229
X-RAY DIFFRACTIONf_angle_d0.442413981
X-RAY DIFFRACTIONf_chiral_restr0.04031642
X-RAY DIFFRACTIONf_plane_restr0.00371810
X-RAY DIFFRACTIONf_dihedral_angle_d3.5121447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.27-3.390.492590.3492323X-RAY DIFFRACTION9.01
3.39-3.530.35440.3172740X-RAY DIFFRACTION21.34
3.53-3.690.3623740.30961533X-RAY DIFFRACTION43.92
3.69-3.880.3641400.29283152X-RAY DIFFRACTION89.31
3.88-4.120.34551530.26553541X-RAY DIFFRACTION99.92
4.12-4.440.26431530.23193559X-RAY DIFFRACTION100
4.44-4.890.28311950.22153530X-RAY DIFFRACTION99.97
4.89-5.590.28251700.24213563X-RAY DIFFRACTION100
5.6-7.050.33712080.27553582X-RAY DIFFRACTION99.97
7.05-54.040.26862030.23083717X-RAY DIFFRACTION99.47

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