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- PDB-2ob4: Human Ubiquitin-Conjugating Enzyme CDC34 -

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Basic information

Entry
Database: PDB / ID: 2ob4
TitleHuman Ubiquitin-Conjugating Enzyme CDC34
ComponentsUbiquitin-conjugating enzyme E2-32 kDa complementing
KeywordsLIGASE / UBL CONJUGATION PATHWAY / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / DNA replication initiation / protein K48-linked ubiquitination / cellular response to interferon-beta / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / G1/S transition of mitotic cell cycle / protein modification process / CLEC7A (Dectin-1) signaling ...(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / DNA replication initiation / protein K48-linked ubiquitination / cellular response to interferon-beta / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / G1/S transition of mitotic cell cycle / protein modification process / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / protein ubiquitination / nucleoplasm / ATP binding / nucleus / 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 ...: / 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 R1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNeculai, D. / Avvakumov, G.V. / Xue, S. / Walker, J.R. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Neculai, D. / Avvakumov, G.V. / Xue, S. / Walker, J.R. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Sicheri, F. / 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 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 28, 2012Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2-32 kDa complementing


Theoretical massNumber of molelcules
Total (without water)20,5001
Polymers20,5001
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.280, 66.310, 124.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-185-

HOH

21A-232-

HOH

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Components

#1: Protein Ubiquitin-conjugating enzyme E2-32 kDa complementing / Ubiquitin-protein ligase / Ubiquitin carrier protein / E2-CDC34


Mass: 20500.164 Da / Num. of mol.: 1 / Fragment: Catalytic Domain: Residues 7-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC34, UBE2R1 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49427, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: The protein was dissolved at 42 mg/ml in 20 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 5% glycerol and 2 mM DTT. Crystals were grown in hanging drops by mixing 2 microL protein solution with 2 microL ...Details: The protein was dissolved at 42 mg/ml in 20 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 5% glycerol and 2 mM DTT. Crystals were grown in hanging drops by mixing 2 microL protein solution with 2 microL well solution (28% PEG 4000, 0.1 M Tris-HCl, pH 8.5, 0.2 M MgCl2, 1 mM DTT and 7.5 mM glycyl-glycyl-glycine) at 21 deg C. For cryoprotection, the crystals were soaked in the well solution supplemented with 25% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 18, 2005
Details: cylindrically bent ULE glass mirror with Pt and Pd coatings
RadiationMonochromator: cryo-cooled Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 7162 / Num. obs: 7162 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.82 % / Rsym value: 0.076 / Net I/σ(I): 2.64
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 417 / Rsym value: 0.32 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→40.03 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.874 / SU B: 12.131 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.551 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28448 359 5 %RANDOM
Rwork0.22323 ---
all0.22637 6802 --
obs0.22637 6802 100 %-
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: 27.773 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--2.58 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 0 70 1344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221333
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9761814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6485159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33823.87162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.47115226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.466158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021027
X-RAY DIFFRACTIONr_nbd_refined0.2070.2589
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.27
X-RAY DIFFRACTIONr_mcbond_it0.5531.5815
X-RAY DIFFRACTIONr_mcangle_it1.01221303
X-RAY DIFFRACTIONr_scbond_it1.2673594
X-RAY DIFFRACTIONr_scangle_it2.154.5511
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 26 -
Rwork0.286 482 -
obs--100 %

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