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- PDB-1jat: Mms2/Ubc13 Ubiquitin Conjugating Enzyme Complex -

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Basic information

Entry
Database: PDB / ID: 1jat
TitleMms2/Ubc13 Ubiquitin Conjugating Enzyme Complex
Components
  • Ubiquitin-Conjugating Enzyme E2-17.5 KDA
  • Ubiquitin-Conjugating Enzyme Variant Mms2
KeywordsLIGASE / ubiquitin / ubiquitin-conjugating enzyme / E2 / UEV
Function / homology
Function and homology information


protein targeting to vacuolar membrane / Interleukin-1 signaling / Aggrephagy / PINK1-PRKN Mediated Mitophagy / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / fungal-type vacuole membrane / DNA damage tolerance ...protein targeting to vacuolar membrane / Interleukin-1 signaling / Aggrephagy / PINK1-PRKN Mediated Mitophagy / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / fungal-type vacuole membrane / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / ligase activity / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / protein K63-linked ubiquitination / protein polyubiquitination / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 13 / Ubiquitin-conjugating enzyme variant MMS2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVanDemark, A.P. / Hofmann, R.M. / Tsui, C. / Pickart, C.M. / Wolberger, C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer.
Authors: VanDemark, A.P. / Hofmann, R.M. / Tsui, C. / Pickart, C.M. / Wolberger, C.
History
DepositionMay 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-Conjugating Enzyme E2-17.5 KDA
B: Ubiquitin-Conjugating Enzyme Variant Mms2


Theoretical massNumber of molelcules
Total (without water)33,2782
Polymers33,2782
Non-polymers00
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.158, 63.797, 53.152
Angle α, β, γ (deg.)90.00, 105.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin-Conjugating Enzyme E2-17.5 KDA


Mass: 17573.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Ubc13 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pJY2 / References: UniProt: P52490, ubiquitin-protein ligase
#2: Protein Ubiquitin-Conjugating Enzyme Variant Mms2


Mass: 15703.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Mms2 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pJY2 / References: UniProt: P53152
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 1000, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMHEPES1drop
210 mM1dropNaCl
31 mMEDTA1drop
45 mMbeta-mercaptoethanol1drop
55 %glycerol1drop
610 mg/mlprotein1drop
735 %PEG10001reservoir
850 mMTris1reservoir
92 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9115 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 30, 2000
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9115 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 36093 / Num. obs: 36093 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 23
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.359 / % possible all: 97.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 185078
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1023636.2 / Data cutoff low absF: 0 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1810 5 %RANDOM
Rwork0.203 ---
all-36093 --
obs-36093 98.5 %-
Solvent computationSolvent model: flat model / Bsol: 66.7178 Å2 / ksol: 0.423792 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å2-5.13 Å2
2---1.57 Å20 Å2
3----0.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 0 276 2576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.28
LS refinement shellResolution: 1.6→1.67 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.317 211 4.8 %
Rwork0.29 4144 -
obs-3439 95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.28

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