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- PDB-6r75: Crystal structure of human Ube2T E54R mutant -

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Basic information

Entry
Database: PDB / ID: 6r75
TitleCrystal structure of human Ube2T E54R mutant
ComponentsUbiquitin-conjugating enzyme E2 T
KeywordsLIGASE / DNA repair / E2 / Ubiquitination / allostery
Function / homology
Function and homology information


protein K29-linked ubiquitination / protein K27-linked ubiquitination / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein monoubiquitination / protein K63-linked ubiquitination / protein K48-linked ubiquitination / protein autoubiquitination ...protein K29-linked ubiquitination / protein K27-linked ubiquitination / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein monoubiquitination / protein K63-linked ubiquitination / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Fanconi Anemia Pathway / protein polyubiquitination / ubiquitin-protein transferase activity / DNA repair / ubiquitin protein ligase binding / DNA damage response / chromatin binding / nucleolus / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsChaugule, V.K. / Rennie, M.L. / Walden, H. / Arkinson, C. / Kamarainen, O. / Toth, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UU_12016/12 United Kingdom
European Research CouncilERC-2015-CoG-681582 United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Allosteric mechanism for site-specific ubiquitination of FANCD2.
Authors: Chaugule, V.K. / Arkinson, C. / Rennie, M.L. / Kamarainen, O. / Toth, R. / Walden, H.
History
DepositionMar 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 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: Ubiquitin-conjugating enzyme E2 T


Theoretical massNumber of molelcules
Total (without water)22,8801
Polymers22,8801
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.130, 46.190, 74.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 T / Cell proliferation-inducing gene 50 protein / E2 ubiquitin-conjugating enzyme T / Ubiquitin carrier ...Cell proliferation-inducing gene 50 protein / E2 ubiquitin-conjugating enzyme T / Ubiquitin carrier protein T / Ubiquitin-protein ligase T


Mass: 22880.250 Da / Num. of mol.: 1 / Mutation: E54R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2T, HSPC150, PIG50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NPD8, E2 ubiquitin-conjugating enzyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 8.5, 20% v/v glycerol ethoxylate, 3% v/v poly(ethylene imine)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2→46.19 Å / Num. obs: 9878 / % possible obs: 88.7 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.028 / Rrim(I) all: 0.053 / Net I/σ(I): 16.7 / Num. measured all: 34140 / Scaling rejects: 182
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.053.60.17690.9880.0560.11594.6
8.94-46.193.50.0361370.9990.0210.04287.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.7.3data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yh2

1yh2


Resolution: 2→39.21 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.88 / SU B: 5.057 / SU ML: 0.137 / SU R Cruickshank DPI: 0.2717 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.211
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 451 4.6 %RANDOM
Rwork0.2252 ---
obs0.2271 9330 87.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 67.64 Å2 / Biso mean: 24.326 Å2 / Biso min: 14.21 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å20 Å20 Å2
2---1.08 Å20 Å2
3----1.76 Å2
Refinement stepCycle: final / Resolution: 2→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 0 57 1313
Biso mean---28.65 -
Num. residues----157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131291
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171221
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.6611754
X-RAY DIFFRACTIONr_angle_other_deg1.2441.5762851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9585156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34321.32468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60715225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2511511
X-RAY DIFFRACTIONr_chiral_restr0.0670.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02258
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 29 -
Rwork0.242 736 -
all-765 -
obs--94.1 %

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