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- PDB-5axe: Crystal Structure Analysis of DNA Duplexes containing sulfoamide-... -

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Basic information

Entry
Database: PDB / ID: 5axe
TitleCrystal Structure Analysis of DNA Duplexes containing sulfoamide-bridged nucleic acid (SuNA-NH)
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(LSH)P*AP*CP*GP*C)-3')
KeywordsDNA / A-FORM DNA / SULFONAMIDE-BRIDGED NUCLEIC ACID / SuNA[NH] / ANTISENSE
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.95 Å
AuthorsMitsuoka, Y. / Aoyama, H. / Kugimiya, A. / Fujimura, Y. / Yamamoto, T. / Waki, R. / Wada, F. / Tahara, S. / Sawamura, M. / Noda, M. ...Mitsuoka, Y. / Aoyama, H. / Kugimiya, A. / Fujimura, Y. / Yamamoto, T. / Waki, R. / Wada, F. / Tahara, S. / Sawamura, M. / Noda, M. / Hari, Y. / Obika, S.
CitationJournal: Org.Biomol.Chem. / Year: 2016
Title: Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure.
Authors: Mitsuoka, Y. / Aoyama, H. / Kugimiya, A. / Fujimura, Y. / Yamamoto, T. / Waki, R. / Wada, F. / Tahara, S. / Sawamura, M. / Noda, M. / Hari, Y. / Obika, S.
History
DepositionJul 28, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
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*CP*GP*TP*AP*(LSH)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(LSH)P*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,2722
Polymers6,2722
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-1 kcal/mol
Surface area3840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.685, 42.905, 45.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3136.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.83 Å3/Da / Density % sol: 32.82 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 14, 2014 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.95→23.68 Å / Num. obs: 29154 / % possible obs: 98.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 4.93 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 27.6
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 7 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLM0.2.17data collection
Aimless0.2.17data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I5W

1i5w


Resolution: 0.95→16.35 Å / SU ML: 0.05 / Cross valid method: NONE / σ(F): 1.08 / Phase error: 10.76 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.144 2762 5.03 %
Rwork0.125 --
obs0.126 29154 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.5 Å2
Refinement stepCycle: LAST / Resolution: 0.95→16.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 414 0 140 554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01734
X-RAY DIFFRACTIONf_angle_d1.61138
X-RAY DIFFRACTIONf_dihedral_angle_d16.223322
X-RAY DIFFRACTIONf_chiral_restr0.287128
X-RAY DIFFRACTIONf_plane_restr0.01732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9528-0.96920.13791580.14132521X-RAY DIFFRACTION97
0.9692-0.98680.16561220.12952672X-RAY DIFFRACTION100
0.9868-1.00580.16951400.11992622X-RAY DIFFRACTION100
1.0058-1.02630.12591470.112657X-RAY DIFFRACTION100
1.0263-1.04870.12361650.10512605X-RAY DIFFRACTION100
1.0487-1.0730.13241540.10412636X-RAY DIFFRACTION100
1.073-1.09990.12731270.10632625X-RAY DIFFRACTION100
1.0999-1.12960.11641280.10112692X-RAY DIFFRACTION100
1.1296-1.16280.11491580.10562585X-RAY DIFFRACTION100
1.1628-1.20040.12261520.10362628X-RAY DIFFRACTION100
1.2004-1.24320.13461000.10592703X-RAY DIFFRACTION100
1.2432-1.2930.12491050.11232667X-RAY DIFFRACTION100
1.293-1.35180.14171510.11242629X-RAY DIFFRACTION100
1.3518-1.42310.1431520.12232635X-RAY DIFFRACTION100
1.4231-1.51220.14651180.12782648X-RAY DIFFRACTION100
1.5122-1.62880.15611520.12422627X-RAY DIFFRACTION100
1.6288-1.79250.1271260.11812657X-RAY DIFFRACTION100
1.7925-2.05150.13911250.12742657X-RAY DIFFRACTION100
2.0515-2.5830.15251640.14982616X-RAY DIFFRACTION100
2.583-16.3540.18421180.15562084X-RAY DIFFRACTION79

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