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- PDB-5xyn: The crystal structure of Csm2-Psy3-Shu1-Shu2 complex from budding... -

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Basic information

Entry
Database: PDB / ID: 5xyn
TitleThe crystal structure of Csm2-Psy3-Shu1-Shu2 complex from budding yeast
Components
  • Chromosome segregation in meiosis protein 2
  • Platinum sensitivity protein 3
  • Suppressor of HU sensitivity involved in recombination protein 1
  • Suppressor of hydroxyurea sensitivity protein 2
KeywordsDNA BINDING PROTEIN / Comlex / REPLICATION
Function / homology
Function and homology information


Shu complex / positive regulation of single-strand break repair via homologous recombination / 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 / nucleolus ...Shu complex / positive regulation of single-strand break repair via homologous recombination / 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 / nucleolus / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Suppressor of HU sensitivity involved in recombination protein 1 / Suppressor of hydroxyurea sensitivity protein 2 / 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: 3.3 Å
AuthorsZhang, S. / Zhang, T. / Ding, J.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31521061 China
Chinese Academy of SciencesXDB08010302 China
Ministry of Science and Technology of China2013CB910404 China
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural basis for the functional role of the Shu complex in homologous recombination.
Authors: Zhang, S. / Wang, L. / Tao, Y. / Bai, T. / Lu, R. / Zhang, T. / Chen, J. / Ding, J.
History
DepositionJul 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Suppressor of HU sensitivity involved in recombination protein 1
D: Suppressor of hydroxyurea sensitivity protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7685
Polymers96,7034
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-57 kcal/mol
Surface area33650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.240, 174.240, 102.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Platinum sensitivity protein 3


Mass: 28427.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PSY3, YLR376C, L8039.17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12318
#2: Protein Chromosome segregation in meiosis protein 2


Mass: 24983.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CSM2, YIL132C / Production host: Escherichia coli (E. coli) / References: UniProt: P40465
#3: Protein Suppressor of HU sensitivity involved in recombination protein 1


Mass: 17138.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SHU1, YHL006C / Production host: Escherichia coli (E. coli) / References: UniProt: P38751
#4: Protein Suppressor of hydroxyurea sensitivity protein 2


Mass: 26152.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SHU2, YDR078C, D4436 / Production host: Escherichia coli (E. coli) / References: UniProt: P38957
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 4.04 Å3/Da / Density % sol: 69.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris, pH 6.5, 0.2M potassium sodium tartrate, 10% PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 24375 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 53.01 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Χ2: 0.924 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.426.30.69223960.7910.2890.7541.023100
3.42-3.556.30.5130.8710.2150.561.01399.9
3.55-3.726.90.3660.930.1460.3960.993100
3.72-3.916.80.2610.9670.1050.2830.999100
3.91-4.166.70.170.9850.0690.1850.992100
4.16-4.486.40.0970.9930.0410.1060.924100
4.48-4.936.50.0720.9950.030.0790.923100
4.93-5.646.80.0650.9960.0260.0710.84399.8
5.64-7.16.20.0550.9970.0230.060.78499.9
7.1-506.20.0270.9980.0120.030.74499.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data scaling
PDB_EXTRACT3.22data extraction
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 3.3→44.33 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.865 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25426 1223 5.1 %RANDOM
Rwork0.21738 ---
obs0.21929 22654 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.731 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 3.3→44.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6027 0 1 0 6028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196148
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.978333
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.1175732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19224.24283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.902151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8511533
X-RAY DIFFRACTIONr_chiral_restr0.0580.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214546
X-RAY DIFFRACTIONr_gen_planes_other
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.301→3.387 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 62 -
Rwork0.275 1381 -
obs--82.22 %

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