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- PDB-6u75: Crystal Structure of S. Cerevisiae SUMO E3 Ligase SIZ2 -

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Basic information

Entry
Database: PDB / ID: 6u75
TitleCrystal Structure of S. Cerevisiae SUMO E3 Ligase SIZ2
ComponentsE3 SUMO-protein ligase SIZ2
KeywordsLIGASE / SUMO / SIGNAL TRANSDUCTION / REPLICATION / RING E3 / PIAS / SIZ / UBIQUITIN / UBC9 / METAL-BINDING / NUCLEUS / PHOSPHOPROTEIN / UBL CONJUGATION PATHWAY / ZINC-FINGER
Function / homology
Function and homology information


: / DNA double-strand break attachment to nuclear envelope / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / protein sumoylation / chromosome segregation / double-stranded DNA binding / chromatin / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
PINIT domain / PINIT domain superfamily / PINIT domain / PINIT domain profile. / MIZ/SP-RING zinc finger / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / SAP domain superfamily / SAP domain / SAP motif profile. ...PINIT domain / PINIT domain superfamily / PINIT domain / PINIT domain profile. / MIZ/SP-RING zinc finger / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 SUMO-protein ligase SIZ2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsLima, C.D. / Cappadocia, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065872 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118080 United States
CitationJournal: Embo J. / Year: 2021
Title: DNA asymmetry promotes SUMO modification of the single-stranded DNA-binding protein RPA.
Authors: Cappadocia, L. / Kochanczyk, T. / Lima, C.D.
History
DepositionAug 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 SUMO-protein ligase SIZ2
B: E3 SUMO-protein ligase SIZ2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6504
Polymers61,5192
Non-polymers1312
Water70339
1
A: E3 SUMO-protein ligase SIZ2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8252
Polymers30,7591
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 SUMO-protein ligase SIZ2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8252
Polymers30,7591
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.916, 80.689, 76.527
Angle α, β, γ (deg.)90.000, 94.995, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein E3 SUMO-protein ligase SIZ2 / E3 SUMO-protein transferase SIZ2 / SAP and Miz-finger domain-containing protein 2


Mass: 30759.445 Da / Num. of mol.: 2 / Fragment: UNP Residues 154-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NFI1, SIZ2, YOR156C / Production host: Escherichia coli (E. coli)
References: UniProt: Q12216, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 mM Tris-HCl pH8 100 mM NaCl 20% glycerol 1 mM beta-mercaptoethanol 40 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.63→49 Å / Num. obs: 21200 / % possible obs: 94.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 44.61 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.057 / Rrim(I) all: 0.107 / Net I/σ(I): 11.15
Reflection shellResolution: 2.63→2.73 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 5431 / CC1/2: 0.726 / Rpim(I) all: 0.316 / Rrim(I) all: 0.581 / % possible all: 86.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I2D

3i2d


Resolution: 2.63→49 Å / SU ML: 0.3895 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 28.0328
RfactorNum. reflection% reflection
Rfree0.2627 1060 5 %
Rwork0.2178 --
obs0.2201 21188 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.42 Å2
Refinement stepCycle: LAST / Resolution: 2.63→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4196 0 2 39 4237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024300
X-RAY DIFFRACTIONf_angle_d0.48265820
X-RAY DIFFRACTIONf_chiral_restr0.0409649
X-RAY DIFFRACTIONf_plane_restr0.0028735
X-RAY DIFFRACTIONf_dihedral_angle_d16.9881620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.750.31031200.23662333X-RAY DIFFRACTION88.56
2.75-2.90.3441360.2522515X-RAY DIFFRACTION95.19
2.9-3.080.31821270.2642557X-RAY DIFFRACTION95.86
3.08-3.320.3351410.26282461X-RAY DIFFRACTION94.04
3.32-3.650.28351310.23252549X-RAY DIFFRACTION94.73
3.65-4.180.24291280.21912420X-RAY DIFFRACTION92.05
4.18-5.260.22111350.18432654X-RAY DIFFRACTION99.04
5.26-490.22171420.18982639X-RAY DIFFRACTION96.73

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