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- PDB-1jbb: Ubiquitin Conjugating Enzyme, Ubc13 -

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Basic information

Entry
Database: PDB / ID: 1jbb
TitleUbiquitin Conjugating Enzyme, Ubc13
Componentsubiquitin conjugating enzyme E2-17.5 KDA
KeywordsLIGASE / UBIQUITIN / UBIQUITIN-CONJUGATING ENZYME / E2
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 / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionJun 3, 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 1.3Aug 16, 2023Group: 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 E2-17.5 KDA
B: ubiquitin conjugating enzyme E2-17.5 KDA


Theoretical massNumber of molelcules
Total (without water)34,9802
Polymers34,9802
Non-polymers00
Water2,360131
1
A: ubiquitin conjugating enzyme E2-17.5 KDA


Theoretical massNumber of molelcules
Total (without water)17,4901
Polymers17,4901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ubiquitin conjugating enzyme E2-17.5 KDA


Theoretical massNumber of molelcules
Total (without water)17,4901
Polymers17,4901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.960, 129.390, 42.920
Angle α, β, γ (deg.)90.00, 96.42, 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: 17489.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: GST-fusion / Gene: Ubc13 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pJY2 / References: UniProt: P52490, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 5000-MME, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
210 mMHEPES1drop
310 mM1dropNaCl
45 mMdithiothreitol1drop
530 %PEG5000 MME1reservoir
6200 mMammonium sulfate1reservoir
750 mMMES1reservoir
82 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 30, 2000 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 17787 / Num. obs: 17787 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 20.099 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 27.8
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1937 / % possible all: 83.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 55421
Reflection shell
*PLUS
% possible obs: 83.2 %

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Processing

Software
NameClassification
MOLREPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QCQ truncated to ALAs

1qcq


Resolution: 2→40 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2547 913 random
Rwork0.183 --
all-17787 -
obs-17787 -
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 0 131 2475
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008563
X-RAY DIFFRACTIONc_angle_deg1.51586
X-RAY DIFFRACTIONc_dihedral_angle_d
LS refinement shellResolution: 2→2.09 Å
RfactorNum. reflection% reflection
Rfree0.268 125 -
Rwork0.2293 --
obs-1957 83.2 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.268

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