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

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Basic information

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


heteroduplex formation / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / telomere maintenance via telomere lengthening / Removal of the Flap Intermediate / telomere maintenance via recombination / Translesion Synthesis by POLH / Activation of the pre-replicative complex / Translesion synthesis by REV1 ...heteroduplex formation / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / telomere maintenance via telomere lengthening / Removal of the Flap Intermediate / telomere maintenance via recombination / Translesion Synthesis by POLH / Activation of the pre-replicative complex / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / single-stranded telomeric DNA binding / Activation of ATR in response to replication stress / mitotic recombination / Termination of translesion DNA synthesis / reciprocal meiotic recombination / DNA unwinding involved in DNA replication / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA topological change / Dual incision in TC-NER / telomere maintenance via telomerase / telomere maintenance / condensed nuclear chromosome / DNA damage checkpoint signaling / nucleotide-excision repair / double-strand break repair via homologous recombination / establishment of protein localization / chromatin organization / single-stranded DNA binding / double-stranded DNA binding / DNA replication / sequence-specific DNA binding / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / DNA repair / mRNA binding / nucleus / metal ion binding / 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 / SAD / Resolution: 1.94 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

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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)57,2968
Polymers57,1274
Non-polymers1684
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-62 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.050, 94.940, 170.470
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: 15616.820 Da / Num. of mol.: 2 / Fragment: UNP residues 1-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / 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 (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M ammonium citrate tribasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 41015 / % possible obs: 98 % / Redundancy: 11.4 % / Biso Wilson estimate: 36.95 Å2 / CC1/2: 0.999 / Rsym value: 0.11 / Net I/σ(I): 12.1
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 11 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2799 / CC1/2: 0.605 / Rsym value: 1.573 / % possible all: 91.3

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.94→48.76 Å / Cor.coef. Fo:Fc: 0.9525 / Cor.coef. Fo:Fc free: 0.9362 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.146 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 2046 4.99 %RANDOM
Rwork0.1854 ---
obs0.1871 41015 97.36 %-
Displacement parametersBiso mean: 50.92 Å2
Baniso -1Baniso -2Baniso -3
1--10.2385 Å20 Å20 Å2
2--1.5015 Å20 Å2
3---8.737 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 1.94→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 0 7 202 3915
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013765HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035055HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1442SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes125HARMONIC2
X-RAY DIFFRACTIONt_gen_planes524HARMONIC5
X-RAY DIFFRACTIONt_it3765HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion18.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion480SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4505SEMIHARMONIC4
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2808 121 4.75 %
Rwork0.2408 2424 -
all0.2427 2545 -
obs--97.36 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.84932.115-0.62566.9106-0.02212.6961-0.0359-0.1092-0.16230.60980.01640.06540.32370.01090.01950.03810.02030.0227-0.17590.0305-0.1497-27.040425.408761.3504
24.24552.24550.7014.99560.18342.1421-0.0239-0.52940.72430.3215-0.20190.2671-0.1904-0.04160.2259-0.13280.0225-0.0322-0.1472-0.1018-0.028229.197368.500760.7921
30-0.09710.063900.17490.0784-0.12140.01070.0765-0.0216-0.04830.0382-0.1129-0.02020.16980.1376-0.0414-0.0076-0.03320.0262-0.03591.365152.608112.9239
400.0126-0.05480-0.31391.316-0.07930.02330.0037-0.051-0.0184-0.01950.17120.20480.09780.11680.0140.0267-0.0466-0.0048-0.0679-1.426242.278912.749
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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