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- PDB-4u6l: Crystal structure of DNA/RNA duplex obtained in the presence of [... -

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Basic information

Entry
Database: PDB / ID: 4u6l
TitleCrystal structure of DNA/RNA duplex obtained in the presence of [Co(NH3)6]Cl3 and SrCl2
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 / homologyCOBALT HEXAMMINE(III) / STRONTIUM ION / DNA / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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 / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9795
Polymers5,6432
Non-polymers3363
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-37 kcal/mol
Surface area3540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.520, 48.520, 46.520
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: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na Cacodylate, Hexammine Cobalt Chloride, SrCl2, MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.60366, 1.60546, 1.0
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.603661
21.605461
311
ReflectionRedundancy: 5.43 % / Number: 45147 / Rmerge(I) obs: 0.033 / Χ2: 0.95 / D res high: 2 Å / D res low: 24.28 Å / Num. obs: 8252 / % possible obs: 99.5 / Rejects: 339
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancyRejects
4.324.2810.0150.675.5816
3.424.310.0270.765.3929
2.993.4210.0410.745.4649
2.712.9910.060.765.4647
2.522.7110.080.845.4357
2.372.5210.120.955.4532
2.252.3710.1811.085.3925
2.152.2510.2771.215.4223
2.072.1510.3081.235.426
22.0710.3791.325.335
ReflectionResolution: 1.9→42.02 Å / Num. obs: 4976 / % possible obs: 99.8 % / Redundancy: 10.76 % / Rmerge(I) obs: 0.03 / Χ2: 0.96 / Net I/σ(I): 32.6 / Num. measured all: 53970 / Scaling rejects: 405
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.9-1.9710.830.3166.454935031.1844100
1.97-2.0510.850.2617.754154941.1453100
2.05-2.1410.810.19310.353564901.1561100
2.14-2.2510.910.17711.654224911.263100
2.25-2.3910.910.11114.555535050.9242100
2.39-2.5810.860.08418.354044950.8426100
2.58-2.8410.840.06722.954475000.7927100
2.84-3.2510.60.03937.752834950.7635100
3.25-4.0910.120.01979.850494960.7730100
4.09-42.0210.90.015118.155485070.862498.1

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Phasing

PhasingMethod: MAD
Phasing dmFOM : 0.46 / FOM acentric: 0.46 / FOM centric: 0.51 / Reflection: 4975 / Reflection acentric: 4680 / Reflection centric: 295
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
1.9-20.070.070.0994289943
2-2.40.20.20.141466140264
2.4-2.70.50.510.485480648
2.7-3.40.80.810.783078050
3.4-5.40.930.940.8967161358

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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: 1.9→42.02 Å / FOM work R set: 0.7831 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2752 517 10.4 %
Rwork0.2505 4458 -
obs-4975 99.8 %
Solvent computationBsol: 69.6493 Å2
Displacement parametersBiso max: 101.05 Å2 / Biso mean: 36.1204 Å2 / Biso min: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.427 Å20 Å20 Å2
2--0.427 Å20 Å2
3----0.854 Å2
Refinement stepCycle: final / Resolution: 1.9→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 374 29 60 463
Biso mean--44.25 43.12 -
Num. residues----17
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.268
X-RAY DIFFRACTIONc_mcbond_it1.7241.5
X-RAY DIFFRACTIONc_mcangle_it2.3282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.3465520.345449X-RAY DIFFRACTION100
1.97-2.050.3246680.3106426X-RAY DIFFRACTION100
2.05-2.140.4005450.3325443X-RAY DIFFRACTION100
2.14-2.250.3785470.3641448X-RAY DIFFRACTION100
2.25-2.390.2918450.3429460X-RAY DIFFRACTION100
2.39-2.580.4266540.3289441X-RAY DIFFRACTION100
2.58-2.840.3933490.3096451X-RAY DIFFRACTION100
2.84-3.250.2431560.2421439X-RAY DIFFRACTION100
3.25-4.090.2362550.1965441X-RAY DIFFRACTION100
4.09-42.020.2178460.2103460X-RAY DIFFRACTION97.7
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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