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- PDB-4dt1: Crystal structure of the Psy3-Csm2 complex -

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Basic information

Entry
Database: PDB / ID: 4dt1
TitleCrystal structure of the Psy3-Csm2 complex
Components
  • Chromosome segregation in meiosis protein 2
  • Platinum sensitivity protein 3
KeywordsDNA BINDING PROTEIN / DNA damage repair / protein complex / RecA-like fold
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
ETHANOL / Chromosome segregation in meiosis protein 2 / Platinum sensitivity protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.899 Å
AuthorsTao, Y. / Niu, L. / Teng, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural analysis of Shu proteins reveals a DNA binding role essential for resisting damage
Authors: Tao, Y. / Li, X. / Liu, Y. / Ruan, J. / Qi, S. / Niu, L. / Teng, M.
History
DepositionFeb 20, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Mar 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: Chromosome segregation in meiosis protein 2
B: Platinum sensitivity protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7346
Polymers53,5502
Non-polymers1844
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-8 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.123, 50.433, 76.833
Angle α, β, γ (deg.)90.00, 103.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-427-

HOH

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Components

#1: 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 (brewer's yeast)
Strain: S288c / Gene: CSM2 / Production host: Escherichia coli (E. coli) / References: UniProt: P40465
#2: Protein Platinum sensitivity protein 3


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: S288c / Gene: PSY3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12318
#3: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris-HCl, 10% Glycerol, 14% ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U11
SYNCHROTRONBSRF 3W1A20.9790, 0.9793, 0.9000
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDOct 15, 2009
MARMOSAIC 225 mm CCD2CCDOct 15, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGHTMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
30.97931
40.91
ReflectionResolution: 1.899→50 Å / Num. obs: 38738 / % possible obs: 96.6 %
Reflection shellResolution: 1.899→1.97 Å / % possible all: 84.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.899→33.094 Å / SU ML: 0.25 / σ(F): 1.94 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 1926 4.98 %
Rwork0.1924 --
obs0.1943 38671 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.025 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0364 Å20 Å2-4.1364 Å2
2--5.0425 Å20 Å2
3----5.0061 Å2
Refinement stepCycle: LAST / Resolution: 1.899→33.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 12 133 3270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073212
X-RAY DIFFRACTIONf_angle_d0.994362
X-RAY DIFFRACTIONf_dihedral_angle_d15.7481137
X-RAY DIFFRACTIONf_chiral_restr0.073520
X-RAY DIFFRACTIONf_plane_restr0.004549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8987-1.96660.33791340.26823160X-RAY DIFFRACTION83
1.9666-2.04530.28351560.21413577X-RAY DIFFRACTION94
2.0453-2.13840.24722030.20153651X-RAY DIFFRACTION97
2.1384-2.25110.22711860.18433762X-RAY DIFFRACTION98
2.2511-2.39210.21112010.1813744X-RAY DIFFRACTION99
2.3921-2.57670.24941930.19213761X-RAY DIFFRACTION99
2.5767-2.83590.232230.19353748X-RAY DIFFRACTION99
2.8359-3.24590.23392240.1913772X-RAY DIFFRACTION99
3.2459-4.08830.20432090.17713789X-RAY DIFFRACTION99
4.0883-33.09850.22081970.18763781X-RAY DIFFRACTION96
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)
10.5468-0.66620.57170.9849-0.06242.46210.0179-0.3885-0.16720.05220.01710.2451-0.0028-0.3771-0.02820.0881-0.010.03790.34010.01790.2137-26.778924.466543.9382
21.05720.25550.66080.6732-0.51632.01990.07940.30450.0188-0.186-0.10960.03520.06360.21660.02140.18030.0727-0.02880.2392-0.02040.1486-23.727326.952412.5334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN BB4 - 237
2X-RAY DIFFRACTION2CHAIN AA1 - 213

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