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- PDB-1qcq: UBIQUITIN CONJUGATING ENZYME -

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Basic information

Entry
Database: PDB / ID: 1qcq
TitleUBIQUITIN CONJUGATING ENZYME
ComponentsPROTEIN (UBIQUITIN CONJUGATING ENZYME)
KeywordsLIGASE / UBIQUITIN / UBIQUITIN-CONJUGATING ENZYME / YEAST
Function / homology
Function and homology information


Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / mitochondria-associated ubiquitin-dependent protein catabolic process / cytoplasm protein quality control by the ubiquitin-proteasome system / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ribosome-associated ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity ...Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / mitochondria-associated ubiquitin-dependent protein catabolic process / cytoplasm protein quality control by the ubiquitin-proteasome system / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ribosome-associated ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase complex / rescue of stalled ribosome / ubiquitin binding / protein polyubiquitination / ubiquitin-protein transferase activity / cellular response to heat / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / 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 / 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 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsCook, W.J. / Jeffrey, L.C. / Xu, Y. / Chau, V.
CitationJournal: Biochemistry / Year: 1993
Title: Tertiary structures of class I ubiquitin-conjugating enzymes are highly conserved: crystal structure of yeast Ubc4.
Authors: Cook, W.J. / Jeffrey, L.C. / Xu, Y. / Chau, V.
History
DepositionMay 10, 1999Deposition site: RCSB / Processing site: RCSB
SupersessionMay 17, 1999ID: 2UCE
Revision 1.0May 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (UBIQUITIN CONJUGATING ENZYME)


Theoretical massNumber of molelcules
Total (without water)16,4751
Polymers16,4751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.900, 66.900, 91.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: Protein PROTEIN (UBIQUITIN CONJUGATING ENZYME) / EC 6.3.2.19


Mass: 16474.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P15731, ubiquitin-protein ligase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.51 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 8000, MAGNESIUM ACETATE, CACODYLATE, pH 5.8, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 %PEG80001reservoir
30.2 Mmagnesium acetate1reservoir
40.1 Mcacodylate 1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12951
21
31
41
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
Detector
TypeIDDetectorDate
NICOLET1AREA DETECTORDec 16, 1992
NICOLET2AREA DETECTORDec 17, 1992
NICOLET3AREA DETECTORJan 20, 1993
NICOLET4AREA DETECTORJan 22, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. obs: 5940 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 10.2
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.368 / % possible all: 87
Reflection
*PLUS
Num. measured all: 22434
Reflection shell
*PLUS
% possible obs: 87 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS0.4refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementResolution: 2.7→100 Å / Rfactor Rfree error: 0.016 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.296 325 5.8 %RANDOM
Rwork0.24 ---
obs-5624 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.84 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 0 0 1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it2.442
X-RAY DIFFRACTIONc_scangle_it3.652.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 48 6.5 %
Rwork0.409 686 -
obs--74.1 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PA / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02

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