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- PDB-3gbi: The Rational Design and Structural Analysis of a Self-Assembled T... -

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Basic information

Entry
Database: PDB / ID: 3gbi
TitleThe Rational Design and Structural Analysis of a Self-Assembled Three-Dimensional DNA Crystal
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
KeywordsDNA / nanotechnology / DNA crystals / DNA crossover / designed crystal lattice
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.018 Å
AuthorsBirktoft, J.J. / Zheng, J. / Seeman, N.C.
CitationJournal: 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
DepositionFeb 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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


Theoretical massNumber of molelcules
Total (without water)12,7974
Polymers12,7974
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

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

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


Theoretical massNumber of molelcules
Total (without water)38,39212
Polymers38,39212
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)107.161, 107.161, 93.144
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*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 6457.188 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA strands were synthesized by standard phosphoramidite techniques on an Applied Biosystems 394 DNA synthesizer using trityl-on mode.
#2: DNA chain DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')


Mass: 2082.400 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
Details: DNA strands were synthesized by standard phosphoramidite techniques on an Applied Biosystems 394 DNA synthesizer using trityl-on
#3: DNA chain DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')


Mass: 1825.216 Da / Num. of mol.: 1
Fragment: last 6 residues of a DNA molecule used in experiment, see remark 400 for details.
Source method: obtained synthetically
Details: DNA strands were synthesized by standard phosphoramidite techniques on an Applied Biosystems 394 DNA synthesizer using trityl-on
#4: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')


Mass: 2432.614 Da / Num. of mol.: 1
Fragment: first 8 residues of a DNA molecule used in experiment, see remark 400 for details.
Source method: obtained synthetically
Details: DNA strands were synthesized by standard phosphoramidite techniques on an Applied Biosystems 394 DNA synthesizer using trityl-on
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*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP *CP*A)-3' (#2) 1 STRAND 5'-D(*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP* CP*G)-3' (#3) 3 STRANDS 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3' THE ASYMMETRIC UNIT IS COMPRISED OF ONE FULL #1 STRAND (CHAIN A), 7-RESIDUE REPEATING UNIT OF #2 STRAND (CHAIN B) AND TWO FRAGMENTS OF #3 STRAND (CHAINS C AND D). THE #2 STRAND SELF-ASSOICATES TO FORM A CIRCULAR DNA MOLECULE WITH INTERNAL 3-FOLD SYMMETRY. IT HAS 3 SYMMETRIC AND SEQUENTIAL REPEATING UNITS. CHAIN B IN THE ASYMMETRIC UNIT REPRESENTS ONE OF THESE REPEATING UNITS. CHAINS D (FIRST 8 RESIDUES OF STRAND #3) AND C (NEXT 6 RESIDUES OF STRAND #3) TOGETHER FORM THE THIRD DNA STRAND (#3) OF THE EXPERIMENT. THIS DNA STRAND SPANS TWO ASYMMETRIC UNITS - HENCE IT WAS DIVIDED INTO THE CURRENT CHAINS C AND D FOR CONVENIENT REPRESENTATION. CHAIN C (1_555) IS COVALENTLY LINKED TO CHAIN D OF ANOTHER ASYMMETRIC UNIT (3_555); AND CHAIN D (1_555) IS COVALENTLY LINKED TO CHAIN C OF ANOTHER ASYMMETRIC UNIT (2_555). THE SELECTION OF RESIDUES FROM THE DNA #2 AND #3 ARE DICTATED BY THEIR PROXIMITY (BASE PAIRING) TO CHAIN A.

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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: 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

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2008
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.01→17.3 Å / Num. all: 3341 / Num. obs: 3211 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 199.88 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.9
Reflection shellResolution: 4→4.07 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL2Mapphasing
RefinementResolution: 4.018→17.288 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.83 / σ(F): 0.14 / Stereochemistry target values: ML
Details: In reality all 3211 measured reflections were used in the refinement (using PHENIX). Of these only 2022 had FOBS/SIGMA_FOBS >/= 0.140.
RfactorNum. reflection% reflectionSelection details
Rfree0.309 203 10.04 %Random
Rwork0.24 ---
all0.246 3211 --
obs0.246 2022 61.14 %-
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.001 Å2 / ksol: 0.09 e/Å3
Displacement parametersBiso mean: 80 Å2
Baniso -1Baniso -2Baniso -3
1-63.252 Å20 Å20 Å2
2--63.252 Å20 Å2
3---227.851 Å2
Refinement stepCycle: LAST / Resolution: 4.018→17.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 0 0 855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161052
X-RAY DIFFRACTIONf_angle_d1.3641465
X-RAY DIFFRACTIONf_dihedral_angle_d31.823406
X-RAY DIFFRACTIONf_chiral_restr0.058166
X-RAY DIFFRACTIONf_plane_restr0.00242
LS refinement shellHighest resolution: 4.018 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.309 203 -
Rwork0.24 1819 -
all-2022 -
obs--61 %

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