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- PDB-5v1l: Structure of S-GNA dodecamer -

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Basic information

Entry
Database: PDB / ID: 5v1l
TitleStructure of S-GNA dodecamer
ComponentsRNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)-3')
KeywordsRNA / Glycol Nucleic Acid / GNA / RNA X-ray structure / Nuclease Stability / modified RNA
Function / homologySPERMINE / STRONTIUM ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsPallan, P.S. / 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 2, 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 1.2Aug 16, 2017Group: Refinement description / Category: pdbx_refine / refine / software
Item: _refine.ls_R_factor_R_work / _refine.ls_number_reflns_all ..._refine.ls_R_factor_R_work / _refine.ls_number_reflns_all / _refine.ls_number_reflns_obs / _software.classification
Revision 2.0Jun 22, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp / database_2 ...chem_comp / database_2 / diffrn_radiation_wavelength / entity_poly / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)-3')
B: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)-3')
C: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)-3')
D: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,13313
Polymers15,2294
Non-polymers9039
Water6,017334
1
A: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)-3')
B: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0806
Polymers7,6152
Non-polymers4654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-112 kcal/mol
Surface area4290 Å2
MethodPISA
2
C: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)-3')
D: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0537
Polymers7,6152
Non-polymers4385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-151 kcal/mol
Surface area4400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.951, 46.239, 82.928
Angle α, β, γ (deg.)90.00, 100.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-362-

HOH

21A-369-

HOH

31D-671-

HOH

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Components

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


Mass: 3807.351 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Oligonucleotide (0.6 mM), sodium cacodylate (20 mM, pH 6.0), lithium chloride (20 mM), strontium chloride (40 mM), magnesium chloride (10 mM), spermine tetrahydrochloride (6 mM), and 2- ...Details: Oligonucleotide (0.6 mM), sodium cacodylate (20 mM, pH 6.0), lithium chloride (20 mM), strontium chloride (40 mM), magnesium chloride (10 mM), spermine tetrahydrochloride (6 mM), and 2-methyl-2,4-pentanediol (MPD; 5% (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.2→27.6 Å / Num. obs: 40705 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Net I/σ(I): 32.34

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Processing

Software
NameVersionClassification
MD2MD-2 diffractometer software from EMBL (with LS-CAT developed extensions)data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
SHELXLrefinement
RefinementResolution: 1.2→27.6 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.153 2034 5 %Random
all-38614 --
obs--99.8 %-
Refinement stepCycle: LAST / Resolution: 1.2→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1008 22 334 1364

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