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- PDB-3ubi: The Absence of Tertiary Interactions in a Self-Assembled DNA Crys... -

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Basic information

Entry
Database: PDB / ID: 3ubi
TitleThe Absence of Tertiary Interactions in a Self-Assembled DNA Crystal Structure
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*CP*GP*TP*AP*CP*TP*CP*G)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*AP*GP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*G)-3')
  • DNA (5'-D(P*GP*CP*TP*TP*GP*TP*CP*GP*TP*TP*CP*AP*TP*CP*A)-3')
KeywordsDNA / NANOTECHNOLOGY / DNA CROSSOVER / DESIGNED CRYSTAL LATTICE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.8046 Å
AuthorsNguyen, N. / Birktoft, J.J. / Sha, R. / Wang, T. / Zheng, J. / Constantinou, P.E. / Ginell, S.L. / Chen, Y. / Mao, C. / Seeman, N.C.
Citation
Journal: J.Mol.Recognit. / Year: 2012
Title: The absence of tertiary interactions in a self-assembled DNA crystal structure.
Authors: Nguyen, N. / Birktoft, J.J. / Sha, R. / Wang, T. / Zheng, J. / Constantinou, P.E. / Ginell, S.L. / Chen, Y. / Mao, C. / Seeman, N.C.
#1: Journal: Nature / Year: 2009
Title: From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal.
Authors: Zheng, J. / Birktoft, J.J. / Chen, Y. / Wang, T. / Sha, R. / Constantinou, P.E. / Ginell, S.L. / Mao, C. / Seeman, N.C.
History
DepositionOct 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*CP*GP*TP*AP*CP*TP*CP*G)-3')
D: DNA (5'-D(P*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*G)-3')
B: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*AP*GP*GP*CP*TP*GP*C)-3')
C: DNA (5'-D(P*GP*CP*TP*TP*GP*TP*CP*GP*TP*TP*CP*AP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)18,9774
Polymers18,9774
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*CP*GP*TP*AP*CP*TP*CP*G)-3')
D: DNA (5'-D(P*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*G)-3')
B: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*AP*GP*GP*CP*TP*GP*C)-3')
C: DNA (5'-D(P*GP*CP*TP*TP*GP*TP*CP*GP*TP*TP*CP*AP*TP*CP*A)-3')

A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*CP*GP*TP*AP*CP*TP*CP*G)-3')
D: DNA (5'-D(P*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*G)-3')
B: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*AP*GP*GP*CP*TP*GP*C)-3')
C: DNA (5'-D(P*GP*CP*TP*TP*GP*TP*CP*GP*TP*TP*CP*AP*TP*CP*A)-3')

A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*CP*GP*TP*AP*CP*TP*CP*G)-3')
D: DNA (5'-D(P*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*G)-3')
B: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*AP*GP*GP*CP*TP*GP*C)-3')
C: DNA (5'-D(P*GP*CP*TP*TP*GP*TP*CP*GP*TP*TP*CP*AP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)56,93212
Polymers56,93212
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
Buried area3520 Å2
ΔGint-5 kcal/mol
Surface area11970 Å2
Unit cell
Length a, b, c (Å)169.980, 169.980, 88.638
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsAUTHORS STATE THAT THE CRYSTAL IS AN INFINITE NETWORK MADE FROM THREE DNA STRANDS THAT SELF-ASSOCIATE. IN THE CURRENT ENTRY THE ASYMMETRIC UNIT IS COMPRISED OF 4 CHAINS, 3 OF WHICH ARE FRAGMENTS OF LONGER DNA STRANDS. APPLYING THE SPACE GROUP H3 SYMMETRY OPERATORS (X, Y, Z,), (-Y, X-Y, Z), AND (-X+Y,-X,Z) TO THE CONTENTS OF THE ASYMMETRIC UNIT GENERATES ONE TRIMERIC UNIT OF THE SELF-ASSOCIATED DNA NETWORK. ADDITIONAL DETAILS ABOUT THE CHEMICAL COMPOSITION AND ASSOCIATION ARE INCLUDED IN REMARK 400.

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Components

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


Mass: 4884.168 Da / Num. of mol.: 1
Fragment: THE 16 RESIDUES IS FROM OF THE FIRST PART OF A DNA MOLECULE USED IN EXPERIMENT, SEE REMARK 400 FOR DETAILS.
Source method: obtained synthetically
#2: DNA chain DNA (5'-D(P*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*G)-3')


Mass: 5230.415 Da / Num. of mol.: 1
Fragment: SYMMETRICALLY- AND SEQUENTIALLY REPEATING UNIT OF A CIRCULAR DNA MOLECULES, SEE REMARK 400 FOR DETAILS.
Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*AP*GP*GP*CP*TP*GP*C)-3')


Mass: 4311.801 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain DNA (5'-D(P*GP*CP*TP*TP*GP*TP*CP*GP*TP*TP*CP*AP*TP*CP*A)-3')


Mass: 4550.957 Da / Num. of mol.: 1
Fragment: THE 15 RESIDUES IS FROM OF THE LAST PART OF A DNA MOLECULE USED IN EXPERIMENT, SEE REMARK 400 FOR DETAILS.
Source method: obtained synthetically
Compound detailsTHE STRUCTURE UNIT IS GENERATED FROM 7 DNA STRANDS WHICH FORM A NETWORK UNIT WITH INTERNAL 3-FOLD ...THE STRUCTURE UNIT IS GENERATED FROM 7 DNA STRANDS WHICH FORM A NETWORK UNIT WITH INTERNAL 3-FOLD SYMMETRY. EXTENDING OF THE STRUCTURE UNIT IN 3-D SPACE RESULTS THE CRYSTAL AT R3 SPACE GROUP (REPRESENTED AS H3). THE DNA SEQUENCES OF THE 7 STRANDS ARE: (#1) 3 STRANDS 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*CP*GP*TP*AP*CP*TP*CP*GP*GP* CP*TP*TP*GP*TP*CP*GP*TP*TP*CP*AP*TP*CP*A)-3'; (#2) 1 STRANDS 5'-D(P*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*GP*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*GP*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*G)-3'; (#3) 3 STRANDS 5'-D(*TP*CP*TP*GP*AP*TP*GP*AP*GP*GP*CP*TP*GP*C)-3'). THE ASYMMETRIC UNIT IS COMPRISED OF THE FIRST 16 NUCLEOTIDES OF THE FULL #1 STRAND (CHAIN A), BY THELAST 15 RESIDUES OF THE FULL #1 STRAND (CHAIN C), BY THE FIRST 17 NUCLEOTIDES OF THE #2 STRAND (CHAIN D) AND BY #3 STRAND (CHAIN B). CHAINS A (FIRST 16 RESIDUES OF STRAND #1) AND C (NEXT 15 RESIDUES OF STRAND #1) TOGETHER FORM THE FIRST DNA STRAND (#3) OF THE EXPERIMENT. THIS DNA STRAND SPANS TWO ASYMMETRIC UNITS- HENCE IT WAS DIVIDED INTO THE CURRENT CHAINS A AND C FOR CONVENIENT REPRESENTATION AND CRYSTALLOGRAPHIC COMPUTING. CHAIN A (1_555) IS COVALENTLY LINKED TO CHAIN C OF ANOTHER ASYMMETRIC UNIT (3_555); AND CHAIN C (1_555) IS COVALENTLY LINKED TO CHAIN A OF ANOTHER ASYMMETRIC UNIT (2_555). THE #2 STRAND FORM A CIRCULAR DNA MOLECULE AS A CONSEQUENCE OF INTERNAL 3-FOLD SYMMETRY OF THE TRIANGLE CHAIN D IN THE ASYMMETRIC UNIT REPRESENTS ONE OF THESE REPEATING UNITS. IT HAS 3 SYMMETRIC AND SEQUENTIAL REPEATING UNITS THAT ARE COVALENTLY LINKED TO EACH OTHER VIA THE O3' END OF RESIDUE 17D TO THE O5' END OF RESIDUE 1D) CHAIN D (1_555) IS COVALENTLY LINKED TO CHAIN D OF TWO NEIGHBOURING ASYMMETRIC UNITS (2_555) AND (3_555). THE SELECTION OF RESIDUES FROM THE DNA #2 AND #3 ARE DICTATED BY THEIR PROXIMITY (BASE PAIRING) TO CHAINS A AND C. CHAIN B IN THE ASYMMETRIC UNIT REPRESENTS THE THIRD OF THESE REPEATING UNITS.

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: CRYSTALLIZATION CONDITIONS: GROWN BY VAPOR DIFFUSION WHILE TREATED WITH A CONTROLLED TEMPERATURE GRADIENT FROM 333 DEGS TO 293 DEGS., PH 8.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: GRAPHITE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 6.805→49.069 Å / Num. all: 1413 / Num. obs: 1413 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: dev_873)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.8046→49.069 Å / SU ML: -0 / Isotropic thermal model: Isotropic / σ(F): 0.24 / Phase error: 34.47 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.152 141 9.98 %RANDOM
Rwork0.1385 ---
obs0.1401 1413 86.85 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0.126 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-67.1315 Å20 Å20 Å2
2--67.1315 Å20 Å2
3---811.9265 Å2
Refinement stepCycle: LAST / Resolution: 6.8046→49.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1265 0 0 1265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031416
X-RAY DIFFRACTIONf_angle_d0.8142177
X-RAY DIFFRACTIONf_dihedral_angle_d30.989606
X-RAY DIFFRACTIONf_chiral_restr0.036246
X-RAY DIFFRACTIONf_plane_restr0.00162
LS refinement shellHighest resolution: 6.8046 Å
RfactorNum. reflection% reflection
Rfree0.152 141 -
Rwork0.1385 1272 -
obs--87 %

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