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- PDB-2ucz: UBIQUITIN CONJUGATING ENZYME (UBC7) FROM SACCHAROMYCES CEREVISIAE -

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Basic information

Entry
Database: PDB / ID: 2ucz
TitleUBIQUITIN CONJUGATING ENZYME (UBC7) FROM SACCHAROMYCES CEREVISIAE
ComponentsUBIQUITIN CONJUGATING ENZYME
KeywordsUBIQUITIN CONJUGATION / LIGASE / YEAST
Function / homology
Function and homology information


CUE1-UBC7 ubiquitin-conjugating enzyme complex / Doa10p ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Hrd1p ubiquitin ligase ERAD-L complex / fungal-type cell wall organization / Antigen processing: Ubiquitination & Proteasome degradation / E2 ubiquitin-conjugating enzyme / ERAD pathway / ubiquitin conjugating enzyme activity / response to cadmium ion ...CUE1-UBC7 ubiquitin-conjugating enzyme complex / Doa10p ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Hrd1p ubiquitin ligase ERAD-L complex / fungal-type cell wall organization / Antigen processing: Ubiquitination & Proteasome degradation / E2 ubiquitin-conjugating enzyme / ERAD pathway / ubiquitin conjugating enzyme activity / response to cadmium ion / ubiquitin-protein transferase activity / chromatin organization / ubiquitin-dependent protein catabolic process / protein ubiquitination / endoplasmic reticulum membrane / endoplasmic reticulum / ATP binding / 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, 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 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsCook, W.J. / Chau, V.
CitationJournal: Biochemistry / Year: 1997
Title: Crystal structure of a class I ubiquitin conjugating enzyme (Ubc7) from Saccharomyces cerevisiae at 2.9 angstroms resolution.
Authors: Cook, W.J. / Martin, P.D. / Edwards, B.F. / Yamazaki, R.K. / Chau, V.
History
DepositionNov 7, 1997Processing site: BNL
SupersessionMar 18, 1998ID: 1UCZ
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN CONJUGATING ENZYME


Theoretical massNumber of molelcules
Total (without water)18,5381
Polymers18,5381
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.500, 106.500, 49.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein UBIQUITIN CONJUGATING ENZYME / UBC7


Mass: 18538.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cellular location: CYTOPLASM / Gene: UBC7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02159, ubiquitin-protein ligase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.36 Å3/Da / Density % sol: 72 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: PROTEIN WAS CRYSTALLIZED FROM 0.6 M SODIUM CITRATE, 100 MM HEPES, PH 7.4, USING HANGING DROP TECHNIQUE AT 23 DEG, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.3 Msodium citrate1drop
30.05 MHEPES1drop
40.6 Msodium citrate1reservoir
50.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1994
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.93 Å / Num. obs: 6557 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.154 / Net I/σ(I): 8
Reflection shellResolution: 2.93→3.11 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1 / Rsym value: 0.327 / % possible all: 62
Reflection
*PLUS
Num. measured all: 25491 / Rmerge(I) obs: 0.154
Reflection shell
*PLUS
% possible obs: 62 % / Num. unique obs: 720

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AAK

1aak
PDB Unreleased entry


Resolution: 2.93→100 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: A POSTERIORI / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 354 5.7 %RANDOM
Rwork0.227 ---
obs0.227 6255 86.5 %-
Displacement parametersBiso mean: 26.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.93→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 0 0 1295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.5
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_d1.51
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: 2.93→3.08 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 35 7 %
Rwork0.336 462 -
obs--41.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / 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_deg1.51

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