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- PDB-5omc: Crystal structure of K. lactis Ddc2 N-terminus in complex with S.... -

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Basic information

Entry
Database: PDB / ID: 5omc
TitleCrystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae Rfa1 (K45E mutant) N-OB domain
Components
  • DNA damage checkpoint protein LCD1
  • Replication factor A protein 1
KeywordsPROTEIN BINDING / Oligonucleotide-binding fold / coiled-coil domain / complex / mutant
Function / homology
Function and homology information


heteroduplex formation / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / Removal of the Flap Intermediate / telomere maintenance via telomere lengthening / mitotic recombination / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI ...heteroduplex formation / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / Removal of the Flap Intermediate / telomere maintenance via telomere lengthening / mitotic recombination / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / Activation of the pre-replicative complex / Termination of translesion DNA synthesis / Activation of ATR in response to replication stress / single-stranded telomeric DNA binding / telomere maintenance via recombination / reciprocal meiotic recombination / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA topological change / Dual incision in TC-NER / telomere maintenance via telomerase / telomere maintenance / DNA damage checkpoint signaling / condensed nuclear chromosome / meiotic cell cycle / nucleotide-excision repair / establishment of protein localization / double-strand break repair via homologous recombination / single-stranded DNA binding / chromatin organization / double-stranded DNA binding / sequence-specific DNA binding / damaged DNA binding / chromosome, telomeric region / DNA replication / protein ubiquitination / DNA repair / mRNA binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA damage checkpoint protein, Lcd1 / DNA damage checkpoint protein / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type ...DNA damage checkpoint protein, Lcd1 / DNA damage checkpoint protein / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Replication factor A protein 1 / DNA damage checkpoint protein LCD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Kluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsDeshpande, I. / Seeber, A. / Shimada, K. / Keusch, J.J. / Gut, H. / Gasser, S.M.
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Basis of Mec1-Ddc2-RPA Assembly and Activation on Single-Stranded DNA at Sites of Damage.
Authors: Deshpande, I. / Seeber, A. / Shimada, K. / Keusch, J.J. / Gut, H. / Gasser, S.M.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Replication factor A protein 1
B: Replication factor A protein 1
C: DNA damage checkpoint protein LCD1
D: DNA damage checkpoint protein LCD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7647
Polymers56,6584
Non-polymers1063
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-65 kcal/mol
Surface area27290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.420, 94.590, 170.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Replication factor A protein 1 / RF-A protein 1 / DNA-binding protein BUF2 / Replication protein A 69 kDa DNA-binding subunit / ...RF-A protein 1 / DNA-binding protein BUF2 / Replication protein A 69 kDa DNA-binding subunit / Single-stranded DNA-binding protein


Mass: 15382.277 Da / Num. of mol.: 2 / Fragment: UNP residues 1-132 / Mutation: K45E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RFA1, BUF2, RPA1, YAR007C, FUN3 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22336
#2: Protein DNA damage checkpoint protein LCD1


Mass: 12946.728 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: LCD1, KLLA0C01892g / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6CUV9
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M lithium sulfate monohydrate, 0.1 M Bis-Tris, 25% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 21408 / % possible obs: 92.1 % / Redundancy: 3.77 % / Biso Wilson estimate: 56.98 Å2 / CC1/2: 0.993 / Rsym value: 0.139 / Net I/σ(I): 5.87
Reflection shellResolution: 2.38→2.45 Å / Redundancy: 2.92 % / Mean I/σ(I) obs: 0.99 / Num. unique obs: 1199 / CC1/2: 0.355 / Rsym value: 0.919 / % possible all: 69.9

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OMB

5omb


Resolution: 2.38→47.29 Å / Cor.coef. Fo:Fc: 0.9426 / Cor.coef. Fo:Fc free: 0.9021 / SU R Cruickshank DPI: 0.362 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.38 / SU Rfree Blow DPI: 0.265 / SU Rfree Cruickshank DPI: 0.264
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 1071 5 %RANDOM
Rwork0.2006 ---
obs0.2036 21407 91.75 %-
Displacement parametersBiso mean: 57.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.5581 Å20 Å20 Å2
2---1.3067 Å20 Å2
3---2.8647 Å2
Refine analyzeLuzzati coordinate error obs: 0.345 Å
Refinement stepCycle: 1 / Resolution: 2.38→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 3 92 3673
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013630HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.134873HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1383SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes502HARMONIC5
X-RAY DIFFRACTIONt_it3630HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion20.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion463SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4114SEMIHARMONIC4
LS refinement shellResolution: 2.38→2.5 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2978 118 5 %
Rwork0.2258 2240 -
all0.2292 2358 -
obs--91.75 %
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)
11.0994-0.83480.5765.2177-0.54252.7214-0.00210.13720.0726-0.53520.06240.1151-0.1321-0.0938-0.0603-0.04160.0387-0.004-0.14420.0255-0.05986.4233117.022194.992
24.2454-2.4499-1.73184.31271.40884.0825-0.08150.499-0.4564-0.4601-0.2152-0.04510.32680.06950.2967-0.061-0.02630.0721-0.2557-0.0702-0.033164.337973.924195
30.0153-0.0981-0.014900.31920.0041-0.10220.0147-0.1060.0093-0.11250.06930.1235-0.14750.21470.1073-0.02190.0364-0.09150.00040.017535.576889.5679243
40-0.0287-0.06760-0.5711.7328-0.0701-0.02510.01120.1048-0.066-0.0416-0.21040.2890.13610.0637-0.0142-0.0236-0.0895-0.01580.024132.8328100.119242.706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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