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- PDB-1pzv: Crystal structures of two UBC (E2) enzymes of the ubiquitin-conju... -

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Basic information

Entry
Database: PDB / ID: 1pzv
TitleCrystal structures of two UBC (E2) enzymes of the ubiquitin-conjugating system in Caenorhabditis elegans
ComponentsProbable ubiquitin-conjugating enzyme E2-19 kDa
KeywordsLIGASE / alpha-beta(4)-alpha(3) / core / meander beta-sheet plus one helix 2 / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein polyubiquitination / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP binding
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/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Probable ubiquitin-conjugating enzyme E2 7
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsSchormann, N. / Lin, G. / Li, S. / Symersky, J. / Qiu, S. / Finley, J. / Luo, D. / Stanton, A. / Carson, M. / Luo, M. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Crystal structures of two UBC (E2) enzymes of the ubiquitin-conjugating system in Caenorhabditis elegans
Authors: Schormann, N. / Lin, G. / Li, S. / Symersky, J. / Qiu, S. / Finley, J. / Luo, D. / Stanton, A. / Carson, M. / Luo, M. / DeLucas, L. / Pruett, P. / Nagy, L. / Arabashi, A. / Gray, R. / ...Authors: Schormann, N. / Lin, G. / Li, S. / Symersky, J. / Qiu, S. / Finley, J. / Luo, D. / Stanton, A. / Carson, M. / Luo, M. / DeLucas, L. / Pruett, P. / Nagy, L. / Arabashi, A. / Gray, R. / Johnson, D. / Tsao, J. / Bunzel, B. / Huang, W. / Shang, Q. / Luan, C.-H. / Lu, S. / Zhang, J. / McKinstry, A. / Chen, H.
History
DepositionJul 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ubiquitin-conjugating enzyme E2-19 kDa


Theoretical massNumber of molelcules
Total (without water)18,9631
Polymers18,9631
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.474, 52.184, 68.882
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 Probable ubiquitin-conjugating enzyme E2-19 kDa / Ubiquitin-protein ligase / Ubiquitin carrier protein


Mass: 18962.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: F58A4.10 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P34477, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: PEG 5000 MME, CAPSO, glycerol, potassium thiocyanate, pH 9.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.105 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 10, 2002 / Details: Mirrors
RadiationMonochromator: Double Crystal Monochromator Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. all: 6215 / Num. obs: 6215 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 16
Reflection shellResolution: 2.52→2.59 Å / Rmerge(I) obs: 0.336 / Num. unique all: 601 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UCZ

2ucz


Resolution: 2.52→19.82 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 500016.78 / Data cutoff high rms absF: 500016.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 311 5.8 %RANDOM
Rwork0.241 ---
all0.252 5401 --
obs0.241 5401 85.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.2738 Å2 / ksol: 0.337704 e/Å3
Displacement parametersBiso mean: 68.9 Å2
Baniso -1Baniso -2Baniso -3
1--28.85 Å20 Å20 Å2
2---23.61 Å20 Å2
3---52.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.8 Å
Refinement stepCycle: LAST / Resolution: 2.52→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 0 41 1270
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d1.54
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.622
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.52→2.66 Å / Rfactor Rfree error: 0.082 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.45 30 5.1 %
Rwork0.448 562 -
obs-592 56.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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