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- PDB-7sg9: [mC-mC] DNA mismatch in a self-assembling rhombohedral lattice at... -

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Basic information

Entry
Database: PDB / ID: 7sg9
Title[mC-mC] DNA mismatch in a self-assembling rhombohedral lattice at pH 5.5
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(5CM)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*CP*AP*(5CM)P*AP*CP*A)-3')
  • DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
KeywordsDNA / Tensegrity triangle / self-assembling crystal / metal-mediated mismatch
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.81 Å
AuthorsLu, B. / Vecchioni, S. / Seeman, N.C. / Sha, R. / Ohayon, Y.P.
Funding support United States, 6items
OrganizationGrant numberCountry
Office of Naval Research (ONR)N000141912596 United States
Department of Energy (DOE, United States)DE-SC0007991 United States
National Science Foundation (NSF, United States)2106790 United States
Human Frontier Science Program (HFSP)RPG0010/2017 United States
National Science Foundation (NSF, United States)DMR-1420073 United States
National Aeronautic Space Administration (NASA, United States)2020 NASA Center Innovation Fund United States
CitationJournal: Adv Mater / Year: 2023
Title: Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction.
Authors: Vecchioni, S. / Lu, B. / Livernois, W. / Ohayon, Y.P. / Yoder, J.B. / Yang, C.F. / Woloszyn, K. / Bernfeld, W. / Anantram, M.P. / Canary, J.W. / Hendrickson, W.A. / Rothschild, L.J. / Mao, C. ...Authors: Vecchioni, S. / Lu, B. / Livernois, W. / Ohayon, Y.P. / Yoder, J.B. / Yang, C.F. / Woloszyn, K. / Bernfeld, W. / Anantram, M.P. / Canary, J.W. / Hendrickson, W.A. / Rothschild, L.J. / Mao, C. / Wind, S.J. / Seeman, N.C. / Sha, R.
History
DepositionOct 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(5CM)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*(5CM)P*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)12,7854
Polymers12,7854
Non-polymers00
Water0
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(5CM)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*(5CM)P*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(5CM)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*(5CM)P*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(5CM)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*(5CM)P*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)38,35612
Polymers38,35612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)106.006, 106.006, 93.781
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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


Mass: 6462.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*AP*(5CM)P*AP*CP*A)-3')


Mass: 2065.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')


Mass: 2129.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')


Mass: 2128.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY

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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: 7.46 Å3/Da / Description: Rhombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: MOPS, 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: APS / Beamline: 17-ID / Wavelength: 1.00743 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 3.809→65.603 Å / Num. obs: 2745 / % possible obs: 89.1 % / Redundancy: 10.9 % / Biso Wilson estimate: 257.06 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
3.809-4.09610.60.81960.368159.9
10.307-65.60342.61950.9991100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W6W

5w6w


Resolution: 3.81→32.8 Å / SU ML: 0.231 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 41.8569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3136 138 5.07 %
Rwork0.2314 2583 -
obs0.2346 2721 70.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 231.89 Å2
Refinement stepCycle: LAST / Resolution: 3.81→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 858 0 0 858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059958
X-RAY DIFFRACTIONf_angle_d0.94571471
X-RAY DIFFRACTIONf_chiral_restr0.0479159
X-RAY DIFFRACTIONf_plane_restr0.003342
X-RAY DIFFRACTIONf_dihedral_angle_d36.9364435
LS refinement shellResolution: 3.81→32.8 Å
RfactorNum. reflection% reflection
Rfree0.3136 138 -
Rwork0.2314 2583 -
obs--70.93 %
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)
14.301692290061.85526851676-1.795896707719.02627453009-2.207741942430.906605305664-0.769962356397-0.0666941297669-1.303097237081.446147564152.364632055411.284299198660.689935087554-0.938236752525-1.886516881642.454903263150.160258903164-0.241560401561.662572509660.6369165250161.7447438453-15.0862798871-3.114104040723.5820107861
22.183288204052.74627997644-2.98893496222.02945655892-2.094889397841.765675570020.003006621163994.566124412152.17701085643-1.411493132392.383789956510.8178642012310.913898482693-3.91472085281-1.889222918561.531602686630.2372423591130.01713707602471.940126224240.2895334276661.66643436223-14.3735796468-0.30598070492921.9365037875
38.16492998748-1.71480818244-7.482568884810.828871238899-1.468458802752.17535284047-0.073588098093-0.1303386905232.983871025781.544099639552.36259154697-0.0183864655525-1.58133348017-3.54228115549-1.767560037362.09954239013-0.0509762240465-0.4200970899051.591011369380.8074896284333.57560373752-16.7957423126-20.327740172635.7884343564
47.849692514273.44133699363-1.721052404319.719193779510.5424899996042.05938553573-1.943084648894.039826678630.909062014679-4.306910264914.84530152142-0.0462554676611-2.00234096982-1.44965322754-1.958266166842.34844125438-0.2084752543921.05064678941.765019761680.6549055898132.8418167799-13.443795252719.79946426018.29118314777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 21)AA1 - 21
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 7)BB1 - 7
3X-RAY DIFFRACTION3(chain 'C' and resid 8 through 14)CC8 - 14
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 7)DD1 - 7

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