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- PDB-4rip: BromoUracil substituted structure of intercalation-locked DNA tet... -

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Entry
Database: PDB / ID: 4rip
TitleBromoUracil substituted structure of intercalation-locked DNA tetraplex
ComponentsDNA (5'-D(*AP*CP*(BRU)P*CP*GP*GP*AP*(BRU)P*GP*AP*T)-3')
KeywordsDNA / BromoUracil / homoduplex / intercalation-locked DNA tetraplex
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 7, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,5031
Polymers3,5031
Non-polymers00
Water45025
1
A: DNA (5'-D(*AP*CP*(BRU)P*CP*GP*GP*AP*(BRU)P*GP*AP*T)-3')

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

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

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


Theoretical massNumber of molelcules
Total (without water)14,0124
Polymers14,0124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
crystal symmetry operation12_565x,x-y+1,-z+1/31
Unit cell
Length a, b, c (Å)26.400, 26.400, 166.452
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-115-

HOH

21A-121-

HOH

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Components

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


Mass: 3502.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100 mM MgCl2, 5% PEG400, 30 mM sodium cacodylate, pH 7.4, 8mM cobalt hexamine, 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: 0.9198 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 12, 2014 / Details: mirror
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.03→55.484 Å / Num. obs: 2699 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 2.9
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.196 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CBF1.3data collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→55 Å / SU ML: 0 / σ(F): 1.46 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 194 5.1 %
Rwork0.2324 --
obs0.2328 2422 99.63 %
all-3804 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.03 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2078 Å20 Å2-0 Å2
2--1.2078 Å2-0 Å2
3----2.4155 Å2
Refinement stepCycle: LAST / Resolution: 2.1→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 207 0 25 232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007232
X-RAY DIFFRACTIONf_angle_d1.659356
X-RAY DIFFRACTIONf_dihedral_angle_d39.74699
X-RAY DIFFRACTIONf_chiral_restr0.09837
X-RAY DIFFRACTIONf_plane_restr0.00410
LS refinement shellResolution: 2.1→2.14 Å
RfactorNum. reflection% reflection
Rfree0.2385 194 -
Rwork0.2324 3610 -
obs--100 %

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