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- PDB-3vir: Crystal strcture of Swi5 from fission yeast -

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Basic information

Entry
Database: PDB / ID: 3vir
TitleCrystal strcture of Swi5 from fission yeast
ComponentsMating-type switching protein swi5
KeywordsRECOMBINATION ACTIVATOR / Sfr1
Function / homology
Function and homology information


meiotic strand invasion / meiotic DNA recombinase assembly involved in reciprocal meiotic recombination / Swi5-Sfr1 complex / Swi5-Swi2 complex / meiotic joint molecule formation / gene conversion at mating-type locus / mating type switching / DNA recombinase assembly / DNA strand invasion / ATPase activator activity ...meiotic strand invasion / meiotic DNA recombinase assembly involved in reciprocal meiotic recombination / Swi5-Sfr1 complex / Swi5-Swi2 complex / meiotic joint molecule formation / gene conversion at mating-type locus / mating type switching / DNA recombinase assembly / DNA strand invasion / ATPase activator activity / double-strand break repair via homologous recombination / DNA recombination / identical protein binding
Similarity search - Function
DNA repair protein, Swi5 / Swi5 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Mating-type switching protein swi5
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.7 Å
AuthorsKuwabara, N. / Yamada, N. / Hashimoto, H. / Sato, M. / Iwasaki, H. / Shimizu, T.
CitationJournal: Structure / Year: 2012
Title: Mechanistic insights into the activation of Rad51-mediated strand exchange from the structure of a recombination activator, the Swi5-Sfr1 complex
Authors: Kuwabara, N. / Murayama, Y. / Hashimoto, H. / Kokabu, Y. / Ikeguchi, M. / Sato, M. / Mayanagi, K. / Tsutsui, Y. / Iwasaki, H. / Shimizu, T.
History
DepositionOct 6, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Mating-type switching protein swi5
B: Mating-type switching protein swi5
C: Mating-type switching protein swi5
D: Mating-type switching protein swi5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6416
Polymers39,0564
Non-polymers5852
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-38 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.240, 57.899, 64.432
Angle α, β, γ (deg.)90.00, 96.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Mating-type switching protein swi5 / DNA repair protein swi5


Mass: 9764.057 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972h- / Gene: swi5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UUB7
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 4.2 Å3/Da / Density % sol: 70.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% MPD, 0.1M Tris-HCl, 24.5mM octyl-b-glucoside, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 20, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 18023 / Num. obs: 15572 / % possible obs: 86.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.4
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 4.5 / % possible all: 62.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.6.0113refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.7→19.65 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.875 / SU B: 25.977 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.3106 776 5 %RANDOM
Rwork0.25087 ---
all0.25378 17174 --
obs0.25378 14795 86.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 65.085 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å20 Å2-0.43 Å2
2--3.11 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 40 0 1990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212006
X-RAY DIFFRACTIONr_bond_other_d0.0030.021355
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9762687
X-RAY DIFFRACTIONr_angle_other_deg1.0233353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20325.65292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.58315390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1551510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.526 36 -
Rwork0.357 692 -
obs--58.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
119.6361-4.1522-7.63671.46691.48573.21090.2341-0.39730.02960.0945-0.1508-0.0923-0.14920.2386-0.08330.10240.0499-0.050.4962-0.03220.075915.288815.450520.3677
227.3928-7.786-8.94812.87362.72543.62440.83390.11160.2216-0.3292-0.4408-0.1291-0.3444-0.0193-0.39310.06320.06360.02410.45940.01940.160112.036817.75099.629
39.098-1.32092.60881.6137-0.14471.0022-0.1742-0.16140.00870.1690.16360.1982-0.0091-0.10740.01060.02940.03680.00910.52790.00080.038659.0438-8.082617.5512
415.9811-5.6345.00342.9402-1.70011.62150.26260.33210.1298-0.2476-0.2276-0.0580.12560.1484-0.03510.07870.0727-0.06020.5229-0.01390.08964.9133-9.92627.2958
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 79
2X-RAY DIFFRACTION2B2 - 67
3X-RAY DIFFRACTION3C14 - 66
4X-RAY DIFFRACTION4D10 - 72

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