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- PDB-1y6l: Human ubiquitin conjugating enzyme E2E2 -

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Basic information

Entry
Database: PDB / ID: 1y6l
TitleHuman ubiquitin conjugating enzyme E2E2
ComponentsUbiquitin-conjugating enzyme E2E2
KeywordsLIGASE / Structural Genomics Consortium / UBIQUITIN / UBIQUITIN-CONJUGATING ENZYME / SGC
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / positive regulation of G1/S transition of mitotic cell cycle / protein monoubiquitination / protein K48-linked ubiquitination / ubiquitin-protein transferase activity ...ISG15 transferase activity / ISG15-protein conjugation / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / positive regulation of G1/S transition of mitotic cell cycle / protein monoubiquitination / protein K48-linked ubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / DNA damage response / ATP binding / nucleus
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 E2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Newman, E.M. / Mackenzie, F. / Kozieradzki, I. / Bochkarev, A. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Mol Cell Proteomics / Year: 2012
Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.
Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S.
History
DepositionDec 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 28, 2012Group: Database references
Revision 1.4Aug 23, 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 / 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 E2E2
B: Ubiquitin-conjugating enzyme E2E2
C: Ubiquitin-conjugating enzyme E2E2


Theoretical massNumber of molelcules
Total (without water)49,8423
Polymers49,8423
Non-polymers00
Water6,648369
1
A: Ubiquitin-conjugating enzyme E2E2


Theoretical massNumber of molelcules
Total (without water)16,6141
Polymers16,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-conjugating enzyme E2E2


Theoretical massNumber of molelcules
Total (without water)16,6141
Polymers16,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin-conjugating enzyme E2E2


Theoretical massNumber of molelcules
Total (without water)16,6141
Polymers16,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.109, 36.110, 130.568
Angle α, β, γ (deg.)90.00, 99.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-193-

HOH

DetailsThe biological unit is expected to be a monomer.

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Components

#1: Protein Ubiquitin-conjugating enzyme E2E2 / Ubiquitin-protein ligase E2 / Ubiquitin carrier protein E2 / UbcH8


Mass: 16613.947 Da / Num. of mol.: 3 / Fragment: Residues 55-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2E2, UBCH8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96LR5, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.34 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 2M (NH4)2SO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 22, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→19.26 Å / Num. obs: 39009 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 23.28
Reflection shellResolution: 1.85→1.92 Å / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QCQ

1qcq


Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.315 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24595 1995 5.1 %RANDOM
Rwork0.19174 ---
obs0.19449 37014 90.51 %-
all-37014 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.993 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20.13 Å2
2--2.13 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 0 369 3855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223579
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9694881
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6735441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31823.469147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65515585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5071524
X-RAY DIFFRACTIONr_chiral_restr0.1170.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022715
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21797
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22473
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2302
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0581.52300
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72323651
X-RAY DIFFRACTIONr_scbond_it2.76231485
X-RAY DIFFRACTIONr_scangle_it4.2854.51230
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 130 -
Rwork0.277 2773 -
obs--91.43 %

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