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- PDB-5v2h: RNA octamer containing glycol nucleic acid, SgnT -

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Basic information

Entry
Database: PDB / ID: 5v2h
TitleRNA octamer containing glycol nucleic acid, SgnT
ComponentsRNA (5'-R(*(CBV)P*GP*AP*AP*(ZTH)P*UP*CP*G)-3')
KeywordsRNA / glycol nucleic acid
Function / homologyCOBALT HEXAMMINE(III) / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.08001306231 Å
AuthorsHarp, J.M. / Egli, M.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA.
Authors: Schlegel, M.K. / Foster, D.J. / Kel'in, A.V. / Zlatev, I. / Bisbe, A. / Jayaraman, M. / Lackey, J.G. / Rajeev, K.G. / Charisse, K. / Harp, J. / Pallan, P.S. / Maier, M.A. / Egli, M. / Manoharan, M.
History
DepositionMar 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 2.0Jun 22, 2022Group: Data collection / Database references / Polymer sequence
Category: chem_comp / database_2 / entity_poly
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1May 22, 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(*(CBV)P*GP*AP*AP*(ZTH)P*UP*CP*G)-3')
B: RNA (5'-R(*(CBV)P*GP*AP*AP*(ZTH)P*UP*CP*G)-3')
C: RNA (5'-R(*(CBV)P*GP*AP*AP*(ZTH)P*UP*CP*G)-3')
D: RNA (5'-R(*(CBV)P*GP*AP*AP*(ZTH)P*UP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4316
Polymers10,2464
Non-polymers1852
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-4 kcal/mol
Surface area5240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.029, 31.901, 33.782
Angle α, β, γ (deg.)90.000, 90.461, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-111-

HOH

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Components

#1: RNA chain
RNA (5'-R(*(CBV)P*GP*AP*AP*(ZTH)P*UP*CP*G)-3')


Mass: 2561.448 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.5 mM oligonucleotide, 40 mM sodium chloride, 10 mM magnesium chloride, 10 mM cobalt(III) hexamine chloride, 20 mM sodium cacodylate, 5% 2-methyl-2,4-pentanediol equilibrated against 40% 2- ...Details: 0.5 mM oligonucleotide, 40 mM sodium chloride, 10 mM magnesium chloride, 10 mM cobalt(III) hexamine chloride, 20 mM sodium cacodylate, 5% 2-methyl-2,4-pentanediol equilibrated against 40% 2-methyl-2-4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.91836 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91836 Å / Relative weight: 1
ReflectionResolution: 1.08→33.781 Å / Num. obs: 35479 / % possible obs: 97.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 5.18 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.069 / Net I/σ(I): 10.74
Reflection shellResolution: 1.08→1.119 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2652 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 3532 / CC1/2: 0.822 / Rpim(I) all: 0.2652 / % possible all: 97.14

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000v714data scaling
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.08001306231→33.7809065231 Å / SU ML: 0.0713631076248 / Cross valid method: FREE R-VALUE / σ(F): 1.42213021666 / Phase error: 15.8804008545
RfactorNum. reflection% reflection
Rfree0.156576755314 1761 4.97837333559 %
Rwork0.135587728698 --
obs0.13663673266 35373 97.4194436794 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.8546699308 Å2
Refinement stepCycle: LAST / Resolution: 1.08001306231→33.7809065231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 660 8 247 915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915719927466738
X-RAY DIFFRACTIONf_angle_d1.303197724111115
X-RAY DIFFRACTIONf_chiral_restr0.042518394967144
X-RAY DIFFRACTIONf_plane_restr0.018110505872132
X-RAY DIFFRACTIONf_dihedral_angle_d15.4545883563400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.10920.1792152088011400.1838511558212547X-RAY DIFFRACTION96.8288288288
1.1092-1.14190.1515638843441140.1428349957172586X-RAY DIFFRACTION97.3674720519
1.1419-1.17870.1699055771791440.1323076426232555X-RAY DIFFRACTION97.016534867
1.1787-1.22080.1512420795961190.1266654539552593X-RAY DIFFRACTION97.0651395848
1.2208-1.26970.1500177442971550.1154878190982496X-RAY DIFFRACTION96.610787172
1.2697-1.32750.1385378444941250.1117499797162582X-RAY DIFFRACTION96.7476769121
1.3275-1.39750.1427189801431080.1118669529212509X-RAY DIFFRACTION95.0254175744
1.3975-1.48510.127955950961300.1084687324932638X-RAY DIFFRACTION99.2114695341
1.4851-1.59970.1347893284991530.1103656134072631X-RAY DIFFRACTION99.3221548341
1.5997-1.76070.1325729293121730.108212119532585X-RAY DIFFRACTION98.9239598278
1.7607-2.01550.137483118671380.1208265204582618X-RAY DIFFRACTION98.0085348506
2.0155-2.53910.1801334061451380.1459675074872520X-RAY DIFFRACTION94.8608137045
2.5391-33.79740.1862473961921240.1758033931362752X-RAY DIFFRACTION99.4123746975

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