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- PDB-4u6k: Crystal structure of DNA/RNA duplex containing 2'-4'-BNA-NC -

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Basic information

Entry
Database: PDB / ID: 4u6k
TitleCrystal structure of DNA/RNA duplex containing 2'-4'-BNA-NC
Components
  • DNA (5'-D(*(NCU)P*(NTT)P*CP*TP*TP*CP*TP*(NTT)P*(NCU))-3')
  • RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
KeywordsDNA/RNA / DNA/RNA duplex / antisense / Bridged Nucleic Acid / DNA-RNA complex
Function / homologyCOBALT HEXAMMINE(III) / DNA / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 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_radiation ...computing / diffrn_radiation / diffrn_source / pdbx_struct_oper_list / software
Item: _computing.pdbx_data_reduction_ds / _diffrn_radiation.pdbx_diffrn_protocol ..._computing.pdbx_data_reduction_ds / _diffrn_radiation.pdbx_diffrn_protocol / _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 1.3Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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(*(NCU)P*(NTT)P*CP*TP*TP*CP*TP*(NTT)P*(NCU))-3')
C: RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
D: DNA (5'-D(*(NCU)P*(NTT)P*CP*TP*TP*CP*TP*(NTT)P*(NCU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2257
Polymers11,7424
Non-polymers4833
Water6,395355
1
A: RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
B: DNA (5'-D(*(NCU)P*(NTT)P*CP*TP*TP*CP*TP*(NTT)P*(NCU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1934
Polymers5,8712
Non-polymers3222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-2 kcal/mol
Surface area3680 Å2
MethodPISA
2
C: RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
D: DNA (5'-D(*(NCU)P*(NTT)P*CP*TP*TP*CP*TP*(NTT)P*(NCU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0323
Polymers5,8712
Non-polymers1611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-4 kcal/mol
Surface area3710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.920, 58.960, 102.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

21A-284-

HOH

31B-150-

HOH

41C-204-

HOH

51C-277-

HOH

61C-282-

HOH

71C-292-

HOH

81D-155-

HOH

91D-165-

HOH

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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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*(NCU)P*(NTT)P*CP*TP*TP*CP*TP*(NTT)P*(NCU))-3')


Mass: 2888.994 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8261.06
2
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Na Cacodylate, NaCl, Hexammine Cobalt, MPD

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-17A10.98
SYNCHROTRONPhoton Factory BL-17A21.60465, 1.60830, 0.98
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMay 25, 2013
ADSC QUANTUM 315r2CCDMay 25, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
21.604651
31.60831
ReflectionRedundancy: 3.6 % / Number: 117593 / Rmerge(I) obs: 0.062 / Χ2: 0.98 / D res high: 1.6 Å / D res low: 51.21 Å / Num. obs: 32414 / % possible obs: 95.7 / Rejects: 882
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancyRejects
3.4551.2110.0411.133.58353
2.743.4510.0460.913.62137
2.392.7410.0690.813.6170
2.172.3910.0890.83.653
2.022.1710.1090.873.5944
1.92.0210.1460.93.6150
1.81.910.1720.983.5930
1.721.810.2061.073.644
1.661.7210.2361.123.650
1.61.6610.3231.233.6251
ReflectionResolution: 1.5→25.61 Å / Num. obs: 21282 / % possible obs: 98 % / Redundancy: 6.82 % / Rmerge(I) obs: 0.056 / Χ2: 0.99 / Net I/σ(I): 17.1 / Num. measured all: 146347 / Scaling rejects: 1099
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.5-1.556.980.285.41475821101.092598
1.55-1.627.030.2146.31464420791.023798.2
1.62-1.696.970.167.61478821180.943397.8
1.69-1.786.920.1318.71460621050.854198.8
1.78-1.896.870.11310.41457021130.834498.6
1.89-2.046.830.09412.11475421470.838198.6
2.04-2.246.810.0717.31461721260.9213699
2.24-2.566.770.05922.7149032176117799.4
2.56-3.236.80.04234.21495921781.0715699.5
3.23-25.616.280.03749.21374821301.3836992.4

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Phasing

PhasingMethod: MAD
Phasing dmFOM : 0.64 / FOM acentric: 0.64 / FOM centric: 0.65 / Reflection: 21207 / Reflection acentric: 19193 / Reflection centric: 2014
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
1.5-1.60.170.180.1339323660272
1.6-1.90.560.570.5163195849470
1.9-2.10.780.780.736003292308
2.1-2.70.870.870.7836143243371
2.7-4.30.940.940.9128552466389

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Processing

Software
NameClassification
CrystalCleardata reduction
PHENIXphasing
CNSrefinement
PDB_EXTRACTdata extraction
SOLVEmodel building
d*TREKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→25.61 Å / FOM work R set: 0.8754 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2156 2111 9.7 %
Rwork0.1982 19171 -
obs-21282 98 %
Solvent computationBsol: 45.5582 Å2
Displacement parametersBiso max: 82.04 Å2 / Biso mean: 22.3891 Å2 / Biso min: 8.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.441 Å20 Å20 Å2
2--0.004 Å20 Å2
3----0.445 Å2
Refinement stepCycle: final / Resolution: 1.5→25.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 780 117 355 1252
Biso mean--18.05 35.17 -
Num. residues----32
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_d2.013
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.1532
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it1.5162.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.26492140.25841895X-RAY DIFFRACTION98
1.55-1.620.33151970.24621880X-RAY DIFFRACTION98.2
1.62-1.690.20732120.20391910X-RAY DIFFRACTION97.8
1.69-1.780.23781940.20431909X-RAY DIFFRACTION98.8
1.78-1.890.22832020.20591912X-RAY DIFFRACTION98.6
1.89-2.040.22962270.20851923X-RAY DIFFRACTION98.6
2.04-2.240.21122070.19971920X-RAY DIFFRACTION99
2.24-2.560.22322230.19661951X-RAY DIFFRACTION99.4
2.56-3.230.20752110.20031967X-RAY DIFFRACTION99.5
3.23-25.610.19162240.17661904X-RAY DIFFRACTION92.1
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_201312.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4nco_xplor.param

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