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- PDB-2e2c: E2-C, AN UBIQUITIN CONJUGATING ENZYME REQUIRED FOR THE DESTRUCTIO... -

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Basic information

Entry
Database: PDB / ID: 2e2c
TitleE2-C, AN UBIQUITIN CONJUGATING ENZYME REQUIRED FOR THE DESTRUCTION OF MITOTIC CYCLINS
ComponentsUBIQUITIN CONJUGATING ENZYME
KeywordsUBIQUITIN CONJUGATION / UBIQUITIN CARRIER PROTEIN / THIOESTER BOND / LIGASE
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / cell cycle / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / cell division / ATP binding
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 C
Similarity search - Component
Biological speciesSpisula solidissima (Atlantic surf clam)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJiang, F. / Basavappa, R.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of the cyclin-specific ubiquitin-conjugating enzyme from clam, E2-C, at 2.0 A resolution.
Authors: Jiang, F. / Basavappa, R.
History
DepositionJan 19, 1999Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
SupersessionMar 23, 1999ID: 1E2C, 1BR7
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Mar 20, 2013Group: Advisory
Revision 1.5Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)17,7621
Polymers17,7621
Non-polymers00
Water3,099172
1
A: UBIQUITIN CONJUGATING ENZYME

A: UBIQUITIN CONJUGATING ENZYME


Theoretical massNumber of molelcules
Total (without water)35,5242
Polymers35,5242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Unit cell
Length a, b, c (Å)46.334, 46.334, 150.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-271-

HOH

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Components

#1: Protein UBIQUITIN CONJUGATING ENZYME


Mass: 17762.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spisula solidissima (Atlantic surf clam) / References: UniProt: Q95044, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.64 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %PEG40001reservoir
20.1 MTris-HCl1reservoir
30.2 Mlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: DOUBLE MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 13327 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.7 / % possible all: 92.7
Reflection shell
*PLUS
% possible obs: 92.7 % / Rmerge(I) obs: 0.358

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AAK

1aak
PDB Unreleased entry


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 789 10 %RANDOM
Rwork0.216 ---
obs0.216 13327 99.4 %-
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 0 172 1422
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.297
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.2

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