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- PDB-1fzy: CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE UBIQUITIN CONJUGATI... -

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Basic information

Entry
Database: PDB / ID: 1fzy
TitleCRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE UBIQUITIN CONJUGATING ENZYME 1
ComponentsUBIQUITIN-CONJUGATING ENZYME E2-24 KDA
KeywordsLIGASE / ALPHA-BETA ROLL
Function / homology
Function and homology information


vesicle organization / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity / : / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP binding ...vesicle organization / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity / : / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP binding / nucleus / cytosol
Similarity search - Function
Ubiquitin-conjugating enzyme, C-terminal fungi / Fungal ubiquitin-associated domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / UBA-like superfamily / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme ...Ubiquitin-conjugating enzyme, C-terminal fungi / Fungal ubiquitin-associated domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / UBA-like superfamily / 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 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsGlover, M. / Williams, R.S.
CitationJournal: Structure / Year: 2001
Title: Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail.
Authors: Hamilton, K.S. / Ellison, M.J. / Barber, K.R. / Williams, R.S. / Huzil, J.T. / McKenna, S. / Ptak, C. / Glover, M. / Shaw, G.S.
History
DepositionOct 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 21, 2021Group: Data collection / Derived calculations / Refinement description
Category: refine / struct_biol / struct_sheet
Item: _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _struct_sheet.number_strands
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2-24 KDA
B: UBIQUITIN-CONJUGATING ENZYME E2-24 KDA


Theoretical massNumber of molelcules
Total (without water)33,3942
Polymers33,3942
Non-polymers00
Water5,098283
1
A: UBIQUITIN-CONJUGATING ENZYME E2-24 KDA


Theoretical massNumber of molelcules
Total (without water)16,6971
Polymers16,6971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UBIQUITIN-CONJUGATING ENZYME E2-24 KDA


Theoretical massNumber of molelcules
Total (without water)16,6971
Polymers16,6971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.166, 47.471, 75.776
Angle α, β, γ (deg.)90.00, 92.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer. A non-crystallographically related dimer is found in the asymmetric unit. The significance of this dimer interaction is unknown. The biological assembly is a monomer. A non-crystallographically related dimer is found in the asymmetric unit. The significance of this dimer interaction is unknown.

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Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2-24 KDA


Mass: 16697.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P21734, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 5000-Monomethylether, Ammonium Sulphate, isopropanol, MES buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20-22 ℃ / pH: 7.5 / Method: vapor diffusion / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
220 mMHEPES1drop
3400 mM1dropNaCl
41 mMEDTA1drop
51 mMdithiothreitol1drop
627 %PEG5000 MME1reservoir
79 %isopropanol1reservoir
8100 mMammonium sulfate1reservoir
9100 mMMES1reservoir
105 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 23300 / Num. obs: 23300 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.345 / Num. unique all: 949 / % possible all: 81.1
Reflection
*PLUS
Num. measured all: 85242
Reflection shell
*PLUS
% possible obs: 81.1 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→20 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER (CNS)
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2301 -RANDOM
Rwork0.209 ---
obs0.209 23274 97.8 %-
all-23274 --
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2313 0 0 283 2596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0087
X-RAY DIFFRACTIONc_angle_deg1.274
X-RAY DIFFRACTIONc_improper_angle_d0.872
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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