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

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Basic information

Entry
Database: PDB / ID: 4rby
TitleFirst X-ray structure of RNA containing guanosine phosphorodithioate
Components5'-R(*CP*GP*CP*(2SG)P*AP*AP*UP*UP*AP*GP*CP*G)-3'
KeywordsRNA / phosphorodithioate RNA / guanosine phosphorodithioate / phosphorothioate / guanosine analogue / hydrophobic / backbone
Function / homologySTRONTIUM ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,0613
Polymers3,8861
Non-polymers1752
Water1,802100
1
A: 5'-R(*CP*GP*CP*(2SG)P*AP*AP*UP*UP*AP*GP*CP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)8,1216
Polymers7,7712
Non-polymers3504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2490 Å2
ΔGint-173 kcal/mol
Surface area3990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.932, 35.015, 31.873
Angle α, β, γ (deg.)90.00, 128.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-579-

HOH

21A-586-

HOH

31A-591-

HOH

41A-596-

HOH

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Components

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


Mass: 3885.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Guanosine phosphorodithioate RNA / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SR / STRONTIUM ION


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


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 mM sodium cacodylate, 40 mM sodium chloride, 10 mM barium chloride, 6 mM spermine tetrahydrochloride, 5% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 11, 2012
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.19→50 Å / Num. all: 11477 / Num. obs: 11213 / % possible obs: 97.7 % / Observed criterion σ(I): 5 / Redundancy: 7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 16.49
Reflection shellResolution: 1.19→1.23 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.037 / Mean I/σ(I) obs: 20.71 / Num. unique all: 1012 / % possible all: 88.5

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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: 1.19→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 554 -RANDOM
Rwork0.181 ---
obs-11213 97.7 %-
Refinement stepCycle: LAST / Resolution: 1.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 255 2 100 357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.028

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