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- PDB-4eq6: The crystal structure of Psy3-Csm2 complex from budding yeast -

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Basic information

Entry
Database: PDB / ID: 4eq6
TitleThe crystal structure of Psy3-Csm2 complex from budding yeast
Components
  • Chromosome segregation in meiosis protein 2
  • Platinum sensitivity protein 3
KeywordsDNA BINDING PROTEIN
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShe, Z. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: FEBS Lett. / Year: 2012
Title: Structural and SAXS analysis of the budding yeast SHU-complex proteins
Authors: She, Z. / Gao, Z.Q. / Liu, Y. / Wang, W.J. / Liu, G.F. / Shtykova, E.V. / Xu, J.H. / Dong, Y.H.
History
DepositionApr 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,9592
Polymers54,9592
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-6 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.333, 51.162, 77.049
Angle α, β, γ (deg.)90.00, 103.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-303-

HOH

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Components

#1: Protein Chromosome segregation in meiosis protein 2 /


Mass: 25114.875 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: pCDFDuet / Production host: Escherichia coli (E. coli) / References: UniProt: P40465
#2: Protein Platinum sensitivity protein 3


Mass: 29844.434 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: pCDFDuet / Production host: Escherichia coli (E. coli) / References: UniProt: Q12318
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 47.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Tris-HCl, pH 8.0, 10% ethanol, 10% 2-methyl-2,4-pentadiol (MPD), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 46537 / Num. obs: 43595 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 38.9
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2353 / % possible all: 91.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.855 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 24.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2169 5.05 %RANDOM
Rwork0.2014 ---
all0.2028 44184 --
obs0.2014 42983 89.73 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.963 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6046 Å2-0 Å2-3.5129 Å2
2--9.9376 Å20 Å2
3----7.3329 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 0 162 3332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073233
X-RAY DIFFRACTIONf_angle_d1.1374380
X-RAY DIFFRACTIONf_dihedral_angle_d14.1281184
X-RAY DIFFRACTIONf_chiral_restr0.082518
X-RAY DIFFRACTIONf_plane_restr0.005547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84190.30981530.246730213174100
1.8419-1.88790.30131500.27293023317399
1.8879-1.9390.5525890.46451471156050
1.939-1.9960.29881740.25132989316399
1.996-2.06040.26361570.19930013158100
2.0604-2.1340.23971680.196130343202100
2.134-2.21940.26841320.20422977310999
2.2194-2.32040.2551800.22331499157949
2.3204-2.44270.22611710.20229993170100
2.4427-2.59570.22131390.206530253164100
2.5957-2.79590.24281700.203830303200100
2.7959-3.07710.23031790.212730083187100
3.0771-3.52170.24741530.20343036318999
3.5217-4.43470.17641070.16611830193760
4.4347-29.85920.18711470.18262871301891
Refinement TLS params.Method: refined / Origin x: -16.7614 Å / Origin y: 1.8044 Å / Origin z: -8.4787 Å
111213212223313233
T0.0212 Å2-0.0026 Å20.0112 Å2--0.0079 Å2-0.0258 Å2--0.1083 Å2
L1.4956 °2-0.1556 °20.5839 °2-0.8969 °2-0.4193 °2--3.1858 °2
S0.0209 Å °-0.1549 Å °-0.018 Å °-0.0297 Å °-0.0483 Å °0.1595 Å °0.0561 Å °-0.3202 Å °0.0122 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 213
2X-RAY DIFFRACTION1allB1 - 237
3X-RAY DIFFRACTION1allA301 - 388
4X-RAY DIFFRACTION1allB301 - 374

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