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- PDB-5omd: Crystal structure of S. cerevisiae Ddc2 N-terminal coiled-coil domain -

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Basic information

Entry
Database: PDB / ID: 5omd
TitleCrystal structure of S. cerevisiae Ddc2 N-terminal coiled-coil domain
ComponentsDNA damage checkpoint protein LCD1
KeywordsPROTEIN BINDING / coiled-coil / dimerization
Function / homology
Function and homology information


ATR-ATRIP complex / regulation of double-strand break repair / nucleobase-containing compound metabolic process / nuclear chromosome / telomere maintenance via telomerase / DNA damage checkpoint signaling / establishment of protein localization / chromatin organization / damaged DNA binding / DNA repair ...ATR-ATRIP complex / regulation of double-strand break repair / nucleobase-containing compound metabolic process / nuclear chromosome / telomere maintenance via telomerase / DNA damage checkpoint signaling / establishment of protein localization / chromatin organization / damaged DNA binding / DNA repair / nucleus / cytoplasm
Similarity search - Function
DNA damage checkpoint protein, Lcd1 / DNA damage checkpoint protein
Similarity search - Domain/homology
DNA damage checkpoint protein LCD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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Assembly

Deposited unit
A: DNA damage checkpoint protein LCD1


Theoretical massNumber of molelcules
Total (without water)7,7341
Polymers7,7341
Non-polymers00
Water81145
1
A: DNA damage checkpoint protein LCD1

A: DNA damage checkpoint protein LCD1


Theoretical massNumber of molelcules
Total (without water)15,4682
Polymers15,4682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2610 Å2
ΔGint-29 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.940, 19.890, 30.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

21A-230-

HOH

31A-242-

HOH

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Components

#1: Protein DNA damage checkpoint protein LCD1 / DNA damage checkpoint protein 2 / Lethal / checkpoint-defective / DNA damage-sensitive protein 1


Mass: 7733.979 Da / Num. of mol.: 1 / Fragment: UNP residues 73-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: LCD1, DDC2, PIE1, YDR499W / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04377
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 24% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00005 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 4644 / % possible obs: 99.8 % / Redundancy: 6.08 % / Biso Wilson estimate: 35.69 Å2 / CC1/2: 0.999 / Rsym value: 0.09 / Net I/σ(I): 13.23
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5.72 % / Mean I/σ(I) obs: 2.19 / Num. unique obs: 330 / CC1/2: 0.706 / Rsym value: 0.856 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A92

1a92


Resolution: 2.1→38.98 Å / Cor.coef. Fo:Fc: 0.9406 / Cor.coef. Fo:Fc free: 0.9456 / SU R Cruickshank DPI: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.269 / SU Rfree Blow DPI: 0.209 / SU Rfree Cruickshank DPI: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 558 12.02 %RANDOM
Rwork0.228 ---
obs0.2333 4644 99.87 %-
Displacement parametersBiso mean: 51.81 Å2
Baniso -1Baniso -2Baniso -3
1-5.3516 Å20 Å20 Å2
2---2.6571 Å20 Å2
3----2.6945 Å2
Refine analyzeLuzzati coordinate error obs: 0.347 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms506 0 0 45 551
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01521HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.15692HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d214SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes22HARMONIC2
X-RAY DIFFRACTIONt_gen_planes68HARMONIC5
X-RAY DIFFRACTIONt_it521HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.96
X-RAY DIFFRACTIONt_other_torsion20.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion64SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact663SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.35 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2628 151 12.02 %
Rwork0.2217 1105 -
all0.2268 1256 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: 28.4228 Å / Origin y: 5.3861 Å / Origin z: 14.1176 Å
111213212223313233
T-0.095 Å20.0124 Å2-0.0412 Å2--0.2433 Å20.0653 Å2--0.0678 Å2
L16.0356 °20.6179 °20.4864 °2-0.4724 °20.2653 °2--1.0497 °2
S0.2186 Å °0.3374 Å °-0.649 Å °0.0718 Å °-0.1014 Å °-0.3835 Å °0.0526 Å °0.2044 Å °-0.1172 Å °
Refinement TLS groupSelection details: { A|* }

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