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- PDB-9mtd: [1T7-12] 3D DNA Double Crossover Motif with an Even Number of Hal... -

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Basic information

Entry
Database: PDB / ID: 9mtd
Title[1T7-12] 3D DNA Double Crossover Motif with an Even Number of Half Turns between Junctions
Components
  • DNA (5'-D(*GP*AP*C)-3')
  • DNA (5'-D(*GP*AP*CP*CP*GP*TP*AP*CP*GP*G)-3')
  • DNA (5'-D(*TP*CP*GP*T)-3')
  • DNA (5'-D(*TP*CP*GP*TP*G)-3')
  • DNA (5'-D(P*AP*C)-3')
  • DNA (5'-D(P*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*A)-3')
  • DNA (5'-D(P*TP*GP*TP*AP*CP*G)-3')
KeywordsDNA / Double crossover / DNA nanotechnology / DAE
Function / homology2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsVecchioni, S. / Woloszyn, K. / Ohayon, Y.P. / Sha, R. / Horvath, A.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0007991 United States
National Science Foundation (NSF, United States)GCR-2317843 United States
CitationJournal: To Be Published
Title: 3D DNA Double Crossover Motif with an Even Number of Half Turns between Junctions
Authors: Vecchioni, S. / Woloszyn, K. / Ohayon, Y.P. / Sha, R. / Horvath, A.
History
DepositionJan 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*TP*GP*TP*AP*CP*G)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*A)-3')
D: DNA (5'-D(*GP*AP*CP*CP*GP*TP*AP*CP*GP*G)-3')
E: DNA (5'-D(*TP*CP*GP*T)-3')
G: DNA (5'-D(*GP*AP*C)-3')
H: DNA (5'-D(*TP*CP*GP*TP*G)-3')
I: DNA (5'-D(P*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,66614
Polymers14,1737
Non-polymers4937
Water1267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.780, 42.780, 227.852
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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DNA chain , 7 types, 7 molecules ABDEGHI

#1: DNA chain DNA (5'-D(P*TP*GP*TP*AP*CP*G)-3')


Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*A)-3')


Mass: 4209.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*AP*CP*CP*GP*TP*AP*CP*GP*G)-3')


Mass: 3070.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*CP*GP*T)-3')


Mass: 1181.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*GP*AP*C)-3')


Mass: 886.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(*TP*CP*GP*TP*G)-3')


Mass: 1511.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (5'-D(P*AP*C)-3')


Mass: 557.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 14 molecules

#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-DG / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: dGMP*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 4.21 Å3/Da / Density % sol: 70.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338-293 at 0.4/hr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.58→37.049 Å / Num. obs: 3661 / % possible obs: 85 % / Redundancy: 13.9 % / CC1/2: 0.994 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
2.583-2.8712030.1971
8.5-37.0492030.9911

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→33.3 Å / SU ML: 0.4943 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.4959
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2958 178 4.9 %
Rwork0.2397 3458 -
obs0.2425 3636 49.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.69 Å2
Refinement stepCycle: LAST / Resolution: 2.58→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 949 28 7 984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421083
X-RAY DIFFRACTIONf_angle_d0.6911654
X-RAY DIFFRACTIONf_chiral_restr0.0371188
X-RAY DIFFRACTIONf_plane_restr0.003648
X-RAY DIFFRACTIONf_dihedral_angle_d36.2867492
LS refinement shellResolution: 2.58→33.3 Å
RfactorNum. reflection% reflection
Rfree0.2958 178 -
Rwork0.2397 3458 -
obs--49.25 %
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)
10.4186695467060.110985443237-0.4238921569680.2307423612770.4521905245182.00819452717-0.058333478876-0.1840170459920.005462126008730.06096186173970.107517953591-0.04806707828690.06821479126830.140875159892-0.008394273472490.9209290360820.1981904600380.2490271468180.693999069671-0.1302346173550.4131221340251.31510.6815.879
21.13928367466-0.1225632777050.8930690655460.485067778663-0.2773895179961.420271475130.21481421368-0.245202329497-0.06586598140490.1623355584690.191330194451-0.123438226730.515626167710.00396746783852-0.09077151286090.831387971385-0.03885523464630.05823896953330.431049617802-0.07429794721130.2073512582253.155-0.0372.835
32.391593088520.9076324422992.69376651612.22453023051.293961504284.64174093172-0.329636071467-0.166053607522-0.0428475288429-0.4047726230080.383685589891-0.01938926924560.22420443259-0.2639335109310.05420628384320.8713735976140.141409199856-0.1017432413120.521799745244-0.1208345383530.2901810806325.565-10.1614.913
43.45491009258-0.8982384834191.762587312382.143171722-1.631113647222.93833101594-0.1404307730210.1167734576270.285033200074-0.2804906501950.1804380190130.281064526249-0.028779275795-0.117963051068-0.02619521719580.6625485680190.3889854745470.02648870982860.7017641603280.1494425513980.330432429807-6.80610.92719.477
53.811020327270.4261382099092.376629673262.42109883644-0.823007394062.371323860460.1457021900960.2404486119380.178714553219-0.180245520731-0.0822383750833-0.12198831123-0.0967196448391-0.0317856821485-0.0781707931440.5099323938830.2834392181950.08418331892770.456572864620.07510361129720.2909339153812.241-12.26713.854
67.71167492742-3.06407913219-2.970515942166.931143174190.7230275782022.974906150750.240164936567-0.03253063076260.799636506508-0.0745429313078-0.00914258516138-0.13897371908-0.27208962587-0.0805548784749-0.2096770020580.8105972418970.3503736169340.06552223350660.47578626312-0.002243157554050.403653423152-4.7415.49725.68
70.664512238836-0.315498865164-0.3451438329870.2480658122380.2530213387530.2600775919340.149050703140.06179532155740.08518759472360.04412914172490.00917054868865-0.0007097237871-0.171857728383-0.0884635333265-0.04117175948120.9044641724270.4513418642390.02999428655150.61145640345-0.01128662770590.2886221486236.4-1.47322.123
81.639941891510.110968216175-2.498699990243.96643789633-0.8572470804963.92671835644-0.0391180143049-0.00629053089671-0.12045655138-0.0167510884482-0.08657860445570.0400296202150.7777479482060.05493238776430.09784180589361.020245972490.442590776688-0.2319594831350.708901566433-0.1815729109750.4338492845657.367-11.47626.698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:9 )A1 - 9
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:14 )B1 - 14
3X-RAY DIFFRACTION3( CHAIN D AND RESID 1:10 )D1 - 10
4X-RAY DIFFRACTION4( CHAIN E AND RESID 1:4 )E1 - 4
5X-RAY DIFFRACTION5( CHAIN B AND RESID 101:101 )B101
6X-RAY DIFFRACTION6( CHAIN G AND RESID 1:3 )G1 - 3
7X-RAY DIFFRACTION7( CHAIN H AND RESID 4:8 )H4 - 8
8X-RAY DIFFRACTION8( CHAIN I AND RESID 1:2 )I1 - 2

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