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- PDB-4rim: Native structure of intercalation-locked DNA tetraplex -

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Basic information

Entry
Database: PDB / ID: 4rim
TitleNative structure of intercalation-locked DNA tetraplex
ComponentsDNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*TP*GP*AP*T)-3')
KeywordsDNA / Homo-duplex / Intercalation-locked DNA tetraplex
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTripathi, S.K. / Zhang, D. / Paukstelis, P.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: An intercalation-locked parallel-stranded DNA tetraplex.
Authors: Tripathi, S. / Zhang, D. / Paukstelis, P.J.
History
DepositionOct 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Derived calculations
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Feb 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,3731
Polymers3,3731
Non-polymers00
Water00
1
A: DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*TP*GP*AP*T)-3')

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

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

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


Theoretical massNumber of molelcules
Total (without water)13,4934
Polymers13,4934
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation7_554y,x,-z-1/31
crystal symmetry operation10_554-y,-x,-z-1/31
Unit cell
Length a, b, c (Å)25.310, 25.310, 167.832
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: DNA chain DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*TP*GP*AP*T)-3')


Mass: 3373.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM BaCl2, 20% MPD, 30 mM NaCaco pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2014 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→55.94 Å / Num. obs: 1595 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 7.7 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 2.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 1.4 / Num. unique all: 378 / Rsym value: 0.487 / % possible all: 99

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Processing

Software
NameVersionClassification
CBF1.3data collection
PHASERphasing
REFMAC5.8.0085refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.902 / SU B: 13.738 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30173 156 8.9 %RANDOM
Rwork0.29906 ---
obs0.30146 1595 99.77 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.175 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20.91 Å2-0 Å2
2--1.81 Å2-0 Å2
3----5.88 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 199 0 0 199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.011223
X-RAY DIFFRACTIONr_bond_other_d0.0030.02109
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.178342
X-RAY DIFFRACTIONr_angle_other_deg1.8533259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.229
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02110
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0244
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0784.927221
X-RAY DIFFRACTIONr_scbond_other2.0814.906220
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6187.368342
X-RAY DIFFRACTIONr_long_range_B_refined4.28447.82283
X-RAY DIFFRACTIONr_long_range_B_other4.27647.801284
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 7 -
Rwork0.315 99 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 0.875 Å / Origin y: -1.599 Å / Origin z: -18.389 Å
111213212223313233
T0.0941 Å2-0.016 Å2-0.0141 Å2-0.0228 Å20.018 Å2--0.0661 Å2
L1.4 °2-0.4234 °2-0.1694 °2-0.7594 °20.9384 °2--9.191 °2
S-0.0376 Å °-0.1442 Å °-0.2257 Å °0.1493 Å °0.053 Å °-0.0611 Å °0.2519 Å °-0.0196 Å °-0.0155 Å °

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