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- PDB-4rc0: X-ray structure of RNA containing guanosine phosphorodithioate -

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Basic information

Entry
Database: PDB / ID: 4rc0
TitleX-ray structure of RNA containing guanosine phosphorodithioate
Components5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(A2M)P*(2SG)P*CP*G)-3'
KeywordsRNA / phosphorodithioate RNA / guanosine phosphorodithioate / phosphorothioate / guanosine analogue / hydrophobic / backbone
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: To be Published
Title: Crystal Structure, Stability and siRNA Activity of Phosphorodithioate-Modified RNAs
Authors: Pallan, P.S. / Yang, X. / Sierant, M. / Abeydeera, N.D. / Hassell, T. / Martinez, C. / Janicka, M. / Nawrot, B. / Egli, M.
History
DepositionSep 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Refinement description / Category: pdbx_refine
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(A2M)P*(2SG)P*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)3,9001
Polymers3,9001
Non-polymers00
Water1,24369
1
A: 5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(A2M)P*(2SG)P*CP*G)-3'

A: 5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(A2M)P*(2SG)P*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,7992
Polymers7,7992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)40.914, 34.836, 32.274
Angle α, β, γ (deg.)90.00, 127.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain 5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(A2M)P*(2SG)P*CP*G)-3'


Mass: 3899.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Guanosine phosphorodithioate RNA / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM sodium cacodylate, 40 mM sodium chloride, 6 mM spermine tetrahydrochloride, 5% v/v MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 3, 2013
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. all: 13579 / Num. obs: 12968 / % possible obs: 95.5 % / Observed criterion σ(I): 5 / Redundancy: 6.6 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 49.21
Reflection shellResolution: 1.13→1.17 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.83 / Num. unique all: 1234 / % possible all: 90.7

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBL (with LS-CAT developed extensions)data collection
MOLREP(CCP4)phasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q1R

2q1r


Resolution: 1.13→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 653 -RANDOM
Rwork0.181 ---
obs-12297 95.5 %-
Refinement stepCycle: LAST / Resolution: 1.13→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 255 0 69 324
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.035

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