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- PDB-8wr5: The Crystal Structure of Mms2 from Biortus -

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Basic information

Entry
Database: PDB / ID: 8wr5
TitleThe Crystal Structure of Mms2 from Biortus
ComponentsUbiquitin-conjugating enzyme E2 variant 2
KeywordsLIGASE / Ubl conjugation pathway
Function / homology
Function and homology information


error-free postreplication DNA repair / UBC13-MMS2 complex / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / protein K63-linked ubiquitination / regulation of DNA repair / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint ...error-free postreplication DNA repair / UBC13-MMS2 complex / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / protein K63-linked ubiquitination / regulation of DNA repair / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Formation of Incision Complex in GG-NER / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / protein ubiquitination / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 variant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of Mms2 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S.
History
DepositionOct 13, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 variant 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6014
Polymers16,3811
Non-polymers2203
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area7770 Å2
MethodPISA
2
A: Ubiquitin-conjugating enzyme E2 variant 2
hetero molecules

A: Ubiquitin-conjugating enzyme E2 variant 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2028
Polymers32,7612
Non-polymers4406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1510 Å2
ΔGint-24 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.967, 53.686, 108.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 variant 2 / DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation- ...DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation-promoting factor 1 / EDPF-1 / MMS2 homolog / Vitamin D3-inducible protein


Mass: 16380.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2V2, MMS2, UEV2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15819
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.86 Å3/Da / Density % sol: 33.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Li2SO4,0.1 M NaAC pH5.5,10% PEG 1000,10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953685 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953685 Å / Relative weight: 1
ReflectionResolution: 1.7→36.07 Å / Num. obs: 13856 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.5
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 713

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→33.085 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.464 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2101 704 5.093 %
Rwork0.1777 13120 -
all0.179 --
obs-13824 99.971 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.777 Å2
Baniso -1Baniso -2Baniso -3
1--1.737 Å2-0 Å20 Å2
2--0.289 Å2-0 Å2
3---1.449 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 13 61 1165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121145
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161107
X-RAY DIFFRACTIONr_angle_refined_deg1.241.6661552
X-RAY DIFFRACTIONr_angle_other_deg0.4261.5692567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.58559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37310212
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.731051
X-RAY DIFFRACTIONr_chiral_restr0.060.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021345
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02249
X-RAY DIFFRACTIONr_nbd_refined0.2020.2228
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.2993
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2556
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.251
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.213
X-RAY DIFFRACTIONr_nbd_other0.2390.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.217
X-RAY DIFFRACTIONr_mcbond_it2.3752.928555
X-RAY DIFFRACTIONr_mcbond_other2.3492.926555
X-RAY DIFFRACTIONr_mcangle_it3.2325.257694
X-RAY DIFFRACTIONr_mcangle_other3.2355.26695
X-RAY DIFFRACTIONr_scbond_it3.5353.41590
X-RAY DIFFRACTIONr_scbond_other3.5343.41591
X-RAY DIFFRACTIONr_scangle_it5.6746.037854
X-RAY DIFFRACTIONr_scangle_other5.6716.036855
X-RAY DIFFRACTIONr_lrange_it7.21330.2381287
X-RAY DIFFRACTIONr_lrange_other7.18829.3471277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.261500.253942X-RAY DIFFRACTION100
1.744-1.7920.254550.242927X-RAY DIFFRACTION100
1.792-1.8430.27660.22873X-RAY DIFFRACTION99.8936
1.843-1.90.235450.212900X-RAY DIFFRACTION100
1.9-1.9620.265430.212833X-RAY DIFFRACTION100
1.962-2.0310.223490.182828X-RAY DIFFRACTION100
2.031-2.1070.199460.18801X-RAY DIFFRACTION100
2.107-2.1930.258480.172753X-RAY DIFFRACTION100
2.193-2.290.238330.172762X-RAY DIFFRACTION100
2.29-2.4010.214420.175692X-RAY DIFFRACTION100
2.401-2.530.241280.17678X-RAY DIFFRACTION100
2.53-2.6830.211250.187665X-RAY DIFFRACTION100
2.683-2.8670.234250.172610X-RAY DIFFRACTION100
2.867-3.0940.219270.181585X-RAY DIFFRACTION100
3.094-3.3870.216170.176530X-RAY DIFFRACTION99.8175
3.387-3.7810.19240.168486X-RAY DIFFRACTION100
3.781-4.3570.198250.151416X-RAY DIFFRACTION100
4.357-5.3130.172190.147369X-RAY DIFFRACTION100
5.313-7.4190.235200.193284X-RAY DIFFRACTION100
7.419-33.0850.135170.135186X-RAY DIFFRACTION99.5098

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