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- PDB-3onh: Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactio... -

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Basic information

Entry
Database: PDB / ID: 3onh
TitleCrystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways
ComponentsUbiquitin-activating enzyme E1-like
KeywordsLIGASE / SUMO conjugation / Ubc9
Function / homology
Function and homology information


SUMO activating enzyme complex / SUMO activating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / protein sumoylation / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme ...Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-activating enzyme E1-like
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsWang, J. / Taherbhoy, A.M. / Hunt, H.W. / Seyedin, S.N. / Miller, D.W. / Huang, D.T. / Schulman, B.A.
CitationJournal: Plos One / Year: 2010
Title: Crystal structure of UBA2(ufd)-Ubc9: insights into E1-E2 interactions in Sumo pathways.
Authors: Wang, J. / Taherbhoy, A.M. / Hunt, H.W. / Seyedin, S.N. / Miller, D.W. / Miller, D.J. / Huang, D.T. / Schulman, B.A.
History
DepositionAug 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-activating enzyme E1-like


Theoretical massNumber of molelcules
Total (without water)14,3241
Polymers14,3241
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.192, 80.192, 50.728
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Ubiquitin-activating enzyme E1-like / SMT3-activating enzyme subunit 2 / Polymerase-interacting protein 2


Mass: 14324.036 Da / Num. of mol.: 1 / Fragment: UNP residues 439-563
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBA2, PIP2, UAL1, YDR390C, D9509.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P52488
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 3M (NH4)2SO4, 1% MPD, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2010
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 20193 / Num. obs: 20193 / % possible obs: 94.77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.6→1.66 Å / % possible all: 96.4

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ONG
Resolution: 1.601→40.096 Å / σ(F): 0.15 / Phase error: 18.96 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1781 1041 5.16 %
Rwork0.1596 --
obs0.1619 20193 94.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.878 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8988 Å2-0 Å20 Å2
2---0.8988 Å2-0 Å2
3---1.7975 Å2
Refinement stepCycle: LAST / Resolution: 1.601→40.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 0 81 966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006896
X-RAY DIFFRACTIONf_angle_d0.9821212
X-RAY DIFFRACTIONf_dihedral_angle_d17.956336
X-RAY DIFFRACTIONf_chiral_restr0.064145
X-RAY DIFFRACTIONf_plane_restr0.003157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.601-1.68590.25631220.25452403X-RAY DIFFRACTION80
1.6859-1.79150.26511120.23392602X-RAY DIFFRACTION86
1.7915-1.92970.20141630.20342738X-RAY DIFFRACTION90
1.9297-2.12390.20431530.1852818X-RAY DIFFRACTION94
2.1239-2.4310.18821340.17242864X-RAY DIFFRACTION94
2.431-3.06190.18421750.15682868X-RAY DIFFRACTION94
3.0619-25.36210.1351510.11082879X-RAY DIFFRACTION93

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