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- PDB-1ayz: CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE UBIQUITIN-CONJU... -

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Entry
Database: PDB / ID: 1ayz
TitleCRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE UBIQUITIN-CONJUGATING ENZYME RAD6 (UBC2) AT 2.6A RESOLUTION
ComponentsUBIQUITIN-CONJUGATING ENZYME RAD6
KeywordsUBIQUITIN CONJUGATION / UBIQUITIN-CONJUGATING ENZYME
Function / homology
Function and homology information


MUB1-RAD6-UBR2 ubiquitin ligase complex / RAD6-UBR2 ubiquitin ligase complex / Rad6-Rad18 complex / regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / HULC complex / error-free postreplication DNA repair / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cytoplasm protein quality control by the ubiquitin-proteasome system ...MUB1-RAD6-UBR2 ubiquitin ligase complex / RAD6-UBR2 ubiquitin ligase complex / Rad6-Rad18 complex / regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / HULC complex / error-free postreplication DNA repair / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cytoplasm protein quality control by the ubiquitin-proteasome system / meiotic DNA double-strand break formation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / telomere maintenance via recombination / DNA duplex unwinding / E2 ubiquitin-conjugating enzyme / error-free translesion synthesis / sporulation resulting in formation of a cellular spore / proteasome binding / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / subtelomeric heterochromatin formation / error-prone translesion synthesis / ERAD pathway / mitotic G1 DNA damage checkpoint signaling / DNA-templated transcription termination / double-strand break repair via homologous recombination / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / chromosome, telomeric region / protein ubiquitination / DNA repair / chromatin / ATP binding / nucleus / 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, catalytic domain homologues / 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 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, MOL REP TO PERFORM THREE-FOLD AVERAGING OF SIR MAP / Resolution: 2.6 Å
AuthorsWorthylake, D.K. / Prakash, S. / Prakash, L. / Hill, C.P.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Crystal structure of the Saccharomyces cerevisiae ubiquitin-conjugating enzyme Rad6 at 2.6 A resolution.
Authors: Worthylake, D.K. / Prakash, S. / Prakash, L. / Hill, C.P.
History
DepositionNov 12, 1997Processing site: BNL
Revision 1.0Aug 26, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description
Category: 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME RAD6
B: UBIQUITIN-CONJUGATING ENZYME RAD6
C: UBIQUITIN-CONJUGATING ENZYME RAD6


Theoretical massNumber of molelcules
Total (without water)58,0933
Polymers58,0933
Non-polymers00
Water1,856103
1
A: UBIQUITIN-CONJUGATING ENZYME RAD6


Theoretical massNumber of molelcules
Total (without water)19,3641
Polymers19,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UBIQUITIN-CONJUGATING ENZYME RAD6


Theoretical massNumber of molelcules
Total (without water)19,3641
Polymers19,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UBIQUITIN-CONJUGATING ENZYME RAD6


Theoretical massNumber of molelcules
Total (without water)19,3641
Polymers19,3641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.750, 146.360, 109.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME RAD6 / UBC2


Mass: 19364.291 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06104, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.9 Å3/Da / Density % sol: 68 %
Crystal growpH: 5 / Details: pH 5.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 %(w/w)PEG80001reservoir
250 mMMES1reservoirpH5.0
31 %(w/v)spermine tetrahydrochloride1reservoir
430 mMprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 26012 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 39.5 Å2 / Net I/σ(I): 12.9
Reflection shellResolution: 2.6→2.64 Å / Mean I/σ(I) obs: 3.6 / % possible all: 66.9
Reflection
*PLUS
Num. measured all: 76204 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 66.9 % / Rmerge(I) obs: 0.269

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Processing

Software
NameVersionClassification
AMoREphasing
MLPHAREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIR, MOL REP TO PERFORM THREE-FOLD AVERAGING OF SIR MAP
Starting model: PDB ENTRY 1AAK

1aak
PDB Unreleased entry


Resolution: 2.6→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1311 5 %RANDOM
Rwork0.213 ---
obs0.213 26010 91.3 %-
Displacement parametersBiso mean: 39.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-20 Å
Luzzati sigma a0.48 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 0 103 3802
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
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
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 202 5.4 %
Rwork0.345 3506 -
obs--78.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOPOLOGY
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36

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