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- PDB-4u6m: Crystal structure of DNA/RNA duplex obtained in the presence of S... -

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Basic information

Entry
Database: PDB / ID: 4u6m
TitleCrystal structure of DNA/RNA duplex obtained in the presence of Spermine
Components
  • DNA (5'-D(*(5CM)P*TP*CP*TP*TP*CP*TP*TP*(5CM))-3')
  • RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
KeywordsDNA/RNA / DNA/RNA hybrid duplex / antisense / DNA-RNA complex
Function / homologyDNA / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKondo, J. / Nomura, Y. / Kitahara, Y. / Obika, S. / Torigoe, H.
CitationJournal: Chem.Commun.(Camb.) / Year: 2016
Title: The crystal structure of a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer in complex with the target RNA.
Authors: Kondo, J. / Nomura, Y. / Kitahara, Y. / Obika, S. / Torigoe, H.
History
DepositionJul 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Derived calculations / Refinement description
Category: computing / diffrn_source ...computing / diffrn_source / pdbx_struct_oper_list / software
Item: _computing.pdbx_data_reduction_ds / _diffrn_source.pdbx_synchrotron_site ..._computing.pdbx_data_reduction_ds / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Jul 6, 2022Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
B: DNA (5'-D(*(5CM)P*TP*CP*TP*TP*CP*TP*TP*(5CM))-3')


Theoretical massNumber of molelcules
Total (without water)5,6432
Polymers5,6432
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint1 kcal/mol
Surface area3360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.090, 49.090, 45.990
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: RNA chain RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')


Mass: 2981.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*(5CM)P*TP*CP*TP*TP*CP*TP*TP*(5CM))-3')


Mass: 2660.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Na Cacodylate, Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→42.52 Å / Num. obs: 5022 / % possible obs: 99.8 % / Redundancy: 10.17 % / Rmerge(I) obs: 0.04 / Χ2: 0.94 / Net I/σ(I): 23.2 / Num. measured all: 51463 / Scaling rejects: 386
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.9-1.9710.250.3585.751395001.371299.8
1.97-2.0510.650.2477.653485011.0711100
2.05-2.1410.110.24849694881.1935100
2.14-2.2510.420.1929.553235091.0421100
2.25-2.3910.290.14410.450814920.8820100
2.39-2.5810.390.09915.853145100.8613100
2.58-2.8410.230.08218.551795040.7722100
2.84-3.259.90.0529.250015010.7643100
3.25-4.098.780.0346.746145030.7819699.2
4.09-42.5210.670.0280.954955140.661398.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
CrystalCleardata reduction
PHENIXphasing
CNSrefinement
PDB_EXTRACTdata extraction
PHASERmodel building
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U6L

4u6l


Resolution: 1.9→42.52 Å / FOM work R set: 0.8441 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2334 271 5.4 %
Rwork0.2065 4749 -
obs-5020 99.8 %
Solvent computationBsol: 94.051 Å2
Displacement parametersBiso max: 82.75 Å2 / Biso mean: 35.55 Å2 / Biso min: 21.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.836 Å20 Å20 Å2
2--0.836 Å20 Å2
3----1.672 Å2
Refinement stepCycle: final / Resolution: 1.9→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 374 20 97 491
Biso mean--26.13 52.19 -
Num. residues----17
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.163
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.4082
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.0392.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.3509280.2823470X-RAY DIFFRACTION99.8
1.97-2.050.2663320.276469X-RAY DIFFRACTION100
2.05-2.140.2559250.2685463X-RAY DIFFRACTION100
2.14-2.250.302270.2865482X-RAY DIFFRACTION100
2.25-2.390.332230.2802469X-RAY DIFFRACTION100
2.39-2.580.2421290.269481X-RAY DIFFRACTION100
2.58-2.840.2564160.2413488X-RAY DIFFRACTION100
2.84-3.250.2299390.2161462X-RAY DIFFRACTION100
3.25-4.090.1846280.1615475X-RAY DIFFRACTION99.2
4.09-42.520.2287240.1697490X-RAY DIFFRACTION98.7
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1nco_xplor.param
X-RAY DIFFRACTION2dna-rna_201312.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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