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- PDB-2aak: UBIQUITIN CONJUGATING ENZYME FROM ARABIDOPSIS THALIANA -

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Basic information

Entry
Database: PDB / ID: 2aak
TitleUBIQUITIN CONJUGATING ENZYME FROM ARABIDOPSIS THALIANA
ComponentsUBIQUITIN CONJUGATING ENZYME
KeywordsUBIQUITIN CONJUGATION / LIGASE
Function / homology
Function and homology information


: / : / vegetative to reproductive phase transition of meristem / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA repair ...: / : / vegetative to reproductive phase transition of meristem / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA repair / ATP binding / 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/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsCook, W.J. / Jeffrey, L.C. / Sullivan, M.L. / Vierstra, R.D.
CitationJournal: J.Biol.Chem. / Year: 1992
Title: Three-dimensional structure of a ubiquitin-conjugating enzyme (E2).
Authors: Cook, W.J. / Jeffrey, L.C. / Sullivan, M.L. / Vierstra, R.D.
History
DepositionNov 6, 1997Processing site: BNL
SupersessionMar 18, 1998ID: 1AAK
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 650HELIX IN THE ORIGINAL STRUCTURE (1AAK), RESIDUES 14 - 16 WERE MODELED AS 3/10 HELIX. AN ADDITIONAL ...HELIX IN THE ORIGINAL STRUCTURE (1AAK), RESIDUES 14 - 16 WERE MODELED AS 3/10 HELIX. AN ADDITIONAL RESIDUE HAS NOW BEEN INSERTED, AND THE ENTIRE N-TERMINAL HELIX IS NOW ALPHA HELIX. THE STRUCTURE HAS BEEN REFINED USING ALL THE DATA (NO SIGMA CUTOFF) AND A BULK SOLVENT MODEL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN CONJUGATING ENZYME


Theoretical massNumber of molelcules
Total (without water)17,2981
Polymers17,2981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.800, 44.900, 83.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UBIQUITIN CONJUGATING ENZYME / UBC1


Mass: 17298.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P25865, ubiquitin-protein ligase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 45 %
Crystal growpH: 6.7
Details: PROTEIN WAS CRYSTALLIZED FROM 35% SATURATED AMMONIUM SULFATE IN 50 MM MES, PH 6.7
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Cook, W.J., (1992) J.Mol.Biol., 223, 1183.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
217.5 %(w/v)satammonium sulfate1drop
30.025 MMES1drop
435 %satammonium sulfate1reservoir
50.05 MMES1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1992
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 6377 / % possible obs: 97.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.077
Reflection
*PLUS
Num. measured all: 40453 / Rmerge(I) obs: 0.077

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→100 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.287 343 5.6 %RANDOM
Rwork0.221 ---
obs0.221 6095 93.5 %-
Displacement parametersBiso mean: 21.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 0 0 1203
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.481.5
X-RAY DIFFRACTIONx_mcangle_it2.332
X-RAY DIFFRACTIONx_scbond_it2.332
X-RAY DIFFRACTIONx_scangle_it3.512.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 47 5.5 %
Rwork0.291 810 -
obs--81.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34

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