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- PDB-3vu9: Crystal Structure of Psy3-Csm2 complex -

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Basic information

Entry
Database: PDB / ID: 3vu9
TitleCrystal Structure of Psy3-Csm2 complex
Components
  • Chromosome segregation in meiosis protein 2
  • Platinum sensitivity protein 3
KeywordsDNA BINDING PROTEIN / DNA repair / recombination / meiosis
Function / homology
Function and homology information


positive regulation of single-strand break repair via homologous recombination / Shu complex / error-free postreplication DNA repair / meiotic chromosome segregation / maintenance of rDNA / DNA recombinase assembly / recombinational repair / error-free translesion synthesis / site of double-strand break / nucleus ...positive regulation of single-strand break repair via homologous recombination / Shu complex / error-free postreplication DNA repair / meiotic chromosome segregation / maintenance of rDNA / DNA recombinase assembly / recombinational repair / error-free translesion synthesis / site of double-strand break / nucleus / cytosol / cytoplasm
Similarity search - Function
Shu complex, component Psy3 / Chromosome segregation in meiosis protein 2 / Shu complex component Csm2, DNA-binding / Shu complex component Psy3, DNA-binding description / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromosome segregation in meiosis protein 2 / Platinum sensitivity protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsTawaramoto, M. / Sasanuma, H. / Hosaka, H. / Lao, J.P. / Sanda, E. / Suzuki, M. / Yamashita, E. / Hunter, N. / Shinohara, M. / Nakagawa, A. / Shinohara, A.
CitationJournal: Nat Commun / Year: 2013
Title: A new protein complex promoting the assembly of Rad51 filaments
Authors: Sasanuma, H. / Tawaramoto, M.S. / Lao, J.P. / Hosaka, H. / Sanda, E. / Suzuki, M. / Yamashita, E. / Hunter, N. / Shinohara, M. / Nakagawa, A. / Shinohara, A.
History
DepositionJun 23, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Platinum sensitivity protein 3
B: Chromosome segregation in meiosis protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6744
Polymers53,5502
Non-polymers1242
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-8 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.560, 50.403, 76.350
Angle α, β, γ (deg.)90.00, 102.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

21A-400-

HOH

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Components

#1: Protein Platinum sensitivity protein 3 / PSY3


Mass: 28566.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PSY3, YLR376C, L8039.17 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12318
#2: Protein Chromosome segregation in meiosis protein 2 / / CSMN


Mass: 24983.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CSM2, YIL132C / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40465
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 293 K / Method: hanging drop vapor diffusion / pH: 7
Details: 0.1M Tris-HCl, 30% Ethylene glycol(in case of Se-Met derivative, 25%), 5% polyethylene glycol, pH 7.0, Hanging Drop Vapor Diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC Quantum 270r / Detector: CCD / Date: Jan 25, 2009 / Details: mirrors
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→44.5 Å / Num. all: 45389 / Num. obs: 45389 / % possible obs: 90 % / Observed criterion σ(I): -4 / Redundancy: 3.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→36 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.126 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23119 2300 5.1 %RANDOM
Rwork0.18217 ---
obs0.1847 43029 89.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.467 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å2-1.8 Å2
2--2.35 Å20 Å2
3----1.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.124 Å0.121 Å
Refinement stepCycle: LAST / Resolution: 1.75→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 8 267 3593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0193449
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.281.9794663
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9785412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78324.506162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14715650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3831521
X-RAY DIFFRACTIONr_chiral_restr0.1810.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0212
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_it2.9882.4831645
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.1493.6912052
X-RAY DIFFRACTIONr_scbond_it3.8542.8371804
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 105 -
Rwork0.351 1734 -
obs--49.56 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7164-0.6630.21951.1466-0.14663.27810.0109-0.2688-0.19620.00780.05720.31620.0186-0.4181-0.06820.0351-0.01530.02590.20.02410.17240.0476-5.35643.8041
21.56570.36550.22330.7195-0.78633.60330.04980.2123-0.0318-0.1807-0.09620.06890.11030.07950.04640.11480.0717-0.050.0739-0.04070.071543.4786-2.190712.3317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 239
2X-RAY DIFFRACTION2B3 - 213

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