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- PDB-3goe: Molecular Mimicry of SUMO promotes DNA repair -

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Basic information

Entry
Database: PDB / ID: 3goe
TitleMolecular Mimicry of SUMO promotes DNA repair
ComponentsDNA repair protein rad60
KeywordsRECOMBINATION / REPLICATION / SUMO-like domain / DNA repair / sumoylation / SUMO / genome stability / DNA damage / DNA recombination / Nucleus / Phosphoprotein
Function / homology
Function and homology information


SUMO ligase regulator activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of DNA replication proteins / SUMOylation of DNA damage response and repair proteins / SUMOylation of nuclear envelope proteins / SUMOylation of transcription factors / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins ...SUMO ligase regulator activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of DNA replication proteins / SUMOylation of DNA damage response and repair proteins / SUMOylation of nuclear envelope proteins / SUMOylation of transcription factors / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / replication fork processing / double-strand break repair via homologous recombination / nucleus
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
DNA repair protein rad60
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsPerry, J.J.P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Molecular mimicry of SUMO promotes DNA repair.
Authors: Prudden, J. / Perry, J.J. / Arvai, A.S. / Tainer, J.A. / Boddy, M.N.
History
DepositionMar 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair protein rad60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8332
Polymers9,7931
Non-polymers401
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)81.519, 81.519, 81.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

21A-106-

HOH

31A-155-

HOH

41A-156-

HOH

51A-161-

HOH

61A-179-

HOH

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Components

#1: Protein DNA repair protein rad60 /


Mass: 9793.047 Da / Num. of mol.: 1 / Fragment: UNP residues 332-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: rad60, SPBC1921.02 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9USX3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 0.2M Ca acetate, 100mM HEPES, 24% (w/v) PEG 4000, pH 7.75, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.818 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 10, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.818 Å / Relative weight: 1
ReflectionResolution: 0.97→50 Å / Num. obs: 50503 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 30
Reflection shellResolution: 0.97→1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2UYZ

2uyz


Resolution: 0.97→50 Å / Num. parameters: 6925 / Num. restraintsaints: 8708 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.169 2526 -random
Rwork0.145 ---
obs-47046 95 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refinement stepCycle: LAST / Resolution: 0.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 1 81 1453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d1.3
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0321
X-RAY DIFFRACTIONs_zero_chiral_vol0.091
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.109
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.136
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.065
X-RAY DIFFRACTIONs_approx_iso_adps0.101

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