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- PDB-4ro4: Sequence and structure of a self-assembled 3-D DNA crystal: D(GGA... -

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Basic information

Entry
Database: PDB / ID: 4ro4
TitleSequence and structure of a self-assembled 3-D DNA crystal: D(GGAAACGTTGGAG)
ComponentsD(GGAAACGTTGGAG)
KeywordsDNA / Self-assembling 3D DNA crystal
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsSaoji, M.M. / Paukstelis, P.J.
Citation
Journal: Biopolymers / Year: 2015
Title: Probing the role of sequence in the assembly of three-dimensional DNA crystals.
Authors: Saoji, M. / Zhang, D. / Paukstelis, P.J.
#1: Journal: Chem.Biol. / Year: 2004
Title: Crystal structure of a continuous three-dimensional DNA lattice.
Authors: Paukstelis, P.J. / Nowakowski, J. / Birktoft, J.J. / Seeman, N.C.
History
DepositionOct 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D(GGAAACGTTGGAG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1052
Polymers4,0811
Non-polymers241
Water1448
1
A: D(GGAAACGTTGGAG)
hetero molecules

A: D(GGAAACGTTGGAG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2104
Polymers8,1612
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)40.399, 40.399, 54.627
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
DetailsSynthetic DNA molecule that self-assembles into 3D DNA crystals.

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Components

#1: DNA chain D(GGAAACGTTGGAG)


Mass: 4080.672 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Artificial DNA molecule synthesized using a DNA synthesizer.
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 120mM Magnesium Formate, 50mM Lithium Chloride, 10% MPD, pH none, EVAPORATION, temperature 298K
PH range: none

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.04→34.99 Å / Num. obs: 3261 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 24.3
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 1.3 / Num. unique all: 483

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P1Y

1p1y


Resolution: 2.04→34.99 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 18.584 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25992 277 8.6 %RANDOM
Rwork0.22603 ---
obs0.22913 2952 98.63 %-
Solvent computationIon probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.923 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å2-0 Å2
2---0.26 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.04→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 254 1 8 263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.011286
X-RAY DIFFRACTIONr_bond_other_d0.0020.02135
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.155442
X-RAY DIFFRACTIONr_angle_other_deg1.6083319
X-RAY DIFFRACTIONr_chiral_restr0.0640.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02151
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0262
X-RAY DIFFRACTIONr_scbond_it6.3953.834286
X-RAY DIFFRACTIONr_scbond_other6.3043.799284
X-RAY DIFFRACTIONr_scangle_other8.5635.735440
X-RAY DIFFRACTIONr_long_range_B_refined9.60335.131413
X-RAY DIFFRACTIONr_long_range_B_other9.50134.994412
LS refinement shellResolution: 2.041→2.094 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.626 9 -
Rwork0.51 227 -
obs--95.93 %
Refinement TLS params.Method: refined / Origin x: 11.036 Å / Origin y: -14.769 Å / Origin z: -11.949 Å
111213212223313233
T0.2896 Å2-0.0814 Å2-0.0166 Å2-0.3808 Å2-0.0222 Å2--0.182 Å2
L3.3218 °23.2817 °2-4.0067 °2-7.6906 °2-3.441 °2--11.4319 °2
S-0.7494 Å °-0.0416 Å °-0.323 Å °-1.159 Å °0.4674 Å °-0.4211 Å °0.8166 Å °-0.4045 Å °0.282 Å °

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