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- PDB-2yb6: Native human Rad6 -

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Basic information

Entry
Database: PDB / ID: 2yb6
TitleNative human Rad6
ComponentsUBIQUITIN-CONJUGATING ENZYME E2 B
KeywordsLIGASE / TRANSLESION SYNTHESIS / UBIQUITIN CHAIN SYNTHESIS
Function / homology
Function and homology information


synaptonemal complex organization / positive regulation of reciprocal meiotic recombination / chiasma assembly / negative regulation of post-translational protein modification / sperm axoneme assembly / HULC complex / meiotic telomere clustering / XY body / protein K11-linked ubiquitination / postreplication repair ...synaptonemal complex organization / positive regulation of reciprocal meiotic recombination / chiasma assembly / negative regulation of post-translational protein modification / sperm axoneme assembly / HULC complex / meiotic telomere clustering / XY body / protein K11-linked ubiquitination / postreplication repair / E2 ubiquitin-conjugating enzyme / negative regulation of reproductive process / negative regulation of developmental process / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / ectopic germ cell programmed cell death / protein K48-linked ubiquitination / response to UV / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / replication fork / Recognition of DNA damage by PCNA-containing replication complex / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / chromatin organization / ubiquitin-dependent protein catabolic process / spermatogenesis / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / response to xenobiotic stimulus / DNA repair / apoptotic process / ubiquitin protein ligase binding / DNA damage response / negative regulation of apoptotic process / chromatin / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm
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
BETA-MERCAPTOETHANOL / Ubiquitin-conjugating enzyme E2 B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHibbert, R.G. / Sixma, T.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: E3 Ligase Rad18 Promotes Monoubiquitination Rather Than Ubiquitin Chain Formation by E2 Enzyme Rad6.
Authors: Hibbert, R.G. / Huang, A. / Boelens, R. / Sixma, T.K.
History
DepositionMar 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2 B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4423
Polymers17,3281
Non-polymers1142
Water2,432135
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.050, 48.050, 124.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

21A-2009-

HOH

31A-2117-

HOH

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Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2 B / RAD6 HOMOLOG B / HR6B / HHR6B / UBIQUITIN CARRIER PROTEIN B / UBIQUITIN-CONJUGATING ENZYME E2-17 ...RAD6 HOMOLOG B / HR6B / HHR6B / UBIQUITIN CARRIER PROTEIN B / UBIQUITIN-CONJUGATING ENZYME E2-17 KDA / UBIQUITIN-PROTEIN LIGASE B


Mass: 17328.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63146
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.08 Å3/Da / Density % sol: 41.9 % / Description: NONE
Crystal growpH: 5.5 / Details: pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→44.84 Å / Num. obs: 22429 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0099refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AYZ

1ayz


Resolution: 1.5→32.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.697 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20538 1226 5.2 %RANDOM
Rwork0.16584 ---
obs0.16781 22429 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.082 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.5→32.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 5 135 1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221269
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.961736
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.535160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76424.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59315211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5741510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221007
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3731.5772
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.32921271
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2933497
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1844.5459
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.52331269
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 99 -
Rwork0.157 1582 -
obs--96.17 %

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