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- PDB-6v6r: Crystal Structure of a Bromine Derivatized Self-Assembling DNA Cr... -

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Basic information

Entry
Database: PDB / ID: 6v6r
TitleCrystal Structure of a Bromine Derivatized Self-Assembling DNA Crystal Scaffold with Rhombohedral Symmetry.
Components
  • DNA (5'-D(*CP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*G)-3')
  • DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')
  • DNA (5'-D(P*GP*TP*CP*AP*G)-3')
KeywordsDNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold / Crystal Lattice / Bromine / SAD / Bromo-dU
Function / homologyCACODYLATE ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsSimmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1360635 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM104960 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail.
Authors: Simmons, C.R. / MacCulloch, T. / Zhang, F. / Liu, Y. / Stephanopoulos, N. / Yan, H.
History
DepositionDec 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: DNA (5'-D(*CP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)-3')
A: DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')
C: DNA (5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*G)-3')
D: DNA (5'-D(P*GP*TP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0696
Polymers12,7954
Non-polymers2742
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.806, 115.806, 44.748
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 6358.123 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')


Mass: 2146.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*G)-3')


Mass: 2770.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*CP*AP*G)-3')


Mass: 1520.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
Has ligand of interestN

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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: 4.51 Å3/Da / Density % sol: 72.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Crystallization conditions: 0.5 mL of 50 mM cacodylate pH 6.5 with 100 mM MgCl2, 1 mM cobalt hexamine, and 10% Ethanol was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock.
Temp details: temperature gradient generated from 60 to 25 C at 0.3 degrees per hour

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 12116 / % possible obs: 98.5 % / Redundancy: 2.4 % / Biso Wilson estimate: 83.16 Å2 / CC1/2: 0.93 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.049 / Rrim(I) all: 0.079 / Χ2: 4.404 / Net I/σ(I): 18.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.751.90.6375550.6210.530.8330.54792.5
2.75-2.82.10.3835780.7880.310.4950.57895.7
2.8-2.852.10.396050.7520.3160.5040.63596
2.85-2.912.40.2766030.8760.2150.3510.55298.5
2.91-2.972.50.1896230.9150.1450.2390.84598.9
2.97-3.042.50.1546330.9750.1180.1950.98399.5
3.04-3.122.50.1165900.8750.090.1472.08799.7
3.12-3.22.40.0866180.9890.0670.112.44599
3.2-3.32.50.0745660.9870.0550.0923.67498.3
3.3-3.42.40.1126240.6560.0990.154.60498.1
3.4-3.522.40.0635940.9940.0510.0814.499
3.52-3.662.60.0816240.9880.0610.1025.72899.4
3.66-3.832.60.0866090.9820.0640.1076.17899.8
3.83-4.032.60.0656540.9880.0490.0825.431100
4.03-4.292.50.0566120.9880.0430.0714.568100
4.29-4.622.40.0625800.9880.0480.0796.83299
4.62-5.082.60.0566090.9910.0420.076.38299.8
5.08-5.812.60.0556080.9910.0420.077.91499.7
5.81-7.322.40.0516370.9920.040.06510.02799.2
7.32-502.50.0495940.9920.0390.0638.55498

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→40.865 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 42.02
RfactorNum. reflection% reflection
Rfree0.2786 602 5 %
Rwork0.2416 --
obs0.2435 12050 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 182.54 Å2 / Biso mean: 109.8962 Å2 / Biso min: 52.24 Å2
Refinement stepCycle: final / Resolution: 2.7→40.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 2 0 857
Biso mean--172.38 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005956
X-RAY DIFFRACTIONf_angle_d0.7531467
X-RAY DIFFRACTIONf_chiral_restr0.04166
X-RAY DIFFRACTIONf_plane_restr0.00442
X-RAY DIFFRACTIONf_dihedral_angle_d35.496406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.97160.45941520.4255280096
2.9716-3.40140.29151400.2577281497
3.4014-4.28460.33271480.28072943100
4.2846-40.8650.23861620.20392891100

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