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- PDB-2z5d: Human ubiquitin-conjugating enzyme E2 H -

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Basic information

Entry
Database: PDB / ID: 2z5d
TitleHuman ubiquitin-conjugating enzyme E2 H
ComponentsUbiquitin-conjugating enzyme E2 H
KeywordsLIGASE / UBIQUITIN / UBIQUITIN-CONJUGATING ENZYME / UBE2H / SGC / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process ...(E3-independent) E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsBochkarev, A. / Cui, H. / Walker, J.R. / Newman, E.M. / Mackenzie, F. / Battaile, K.P. / 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
DepositionJul 6, 2007Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 9, 2007ID: 1YH6
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 5, 2012Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Val16 is mutated to ILE16 as result of an unintentional PCR-generated mutation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 H
B: Ubiquitin-conjugating enzyme E2 H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5353
Polymers40,5122
Non-polymers231
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1035.4 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.959, 85.861, 102.558
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 E2 H / Ubiquitin-protein ligase H / Ubiquitin carrier protein H / UbcH2 / E2-20K


Mass: 20255.910 Da / Num. of mol.: 2 / Fragment: residues 1-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2H / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: P62256, ubiquitin-protein ligase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2N NaCl, 0.1M bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2004 / Details: SI(111) DOUBLE CRYSTAL
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→65.8 Å / Num. all: 22884 / Num. obs: 22884 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.7 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→65.8 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.513 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22255 1162 5.1 %RANDOM
Rwork0.18134 ---
obs0.18352 21485 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---1.01 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.1→65.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 1 190 2635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222513
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9743412
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4225301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85824.957115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70315429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.442158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021914
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21156
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21701
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2159
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1810.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8881.51518
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7422471
X-RAY DIFFRACTIONr_scbond_it3.03531033
X-RAY DIFFRACTIONr_scangle_it4.9984.5941
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 99 -
Rwork0.165 1531 -
obs--96.39 %

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