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- PDB-2q1o: Crystal Structure Analysis of the RNA Dodecamer CGC-NF2-AAUUGGCG,... -

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Basic information

Entry
Database: PDB / ID: 2q1o
TitleCrystal Structure Analysis of the RNA Dodecamer CGC-NF2-AAUUGGCG, with an Incorporated 2,4-Difluorotoluyl Residue (NF2)
ComponentsRNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3')
KeywordsRNA / 2 / 4-Difluorotoluyl Nucleoside / Chemical Modification / RNAi / Hydrogen Bond
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsLi, F. / Pallan, P.S.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme.
Authors: Li, F. / Pallan, P.S. / Maier, M.A. / Rajeev, K.G. / Mathieu, S.L. / Kreutz, C. / Fan, Y. / Sanghvi, J. / Micura, R. / Rozners, E. / Manoharan, M. / Egli, M.
History
DepositionMay 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3')
B: RNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3')
C: RNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3')
D: RNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)15,3774
Polymers15,3774
Non-polymers00
Water5,819323
1
A: RNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3')
B: RNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,6892
Polymers7,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
MethodPISA
2
C: RNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3')
D: RNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,6892
Polymers7,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.900, 32.060, 42.930
Angle α, β, γ (deg.)96.24, 83.87, 93.91
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain
RNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3')


Mass: 3844.353 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Droplets containing 0.5 mM oligonucleotide, 0.8 M ammonium sulfate, 0.05 M MES, pH 6.0, were equilibrated against a reservoir of 1.6 M ammonium sulfate, 0.1 M MES, pH 6.0. , VAPOR DIFFUSION, ...Details: Droplets containing 0.5 mM oligonucleotide, 0.8 M ammonium sulfate, 0.05 M MES, pH 6.0, were equilibrated against a reservoir of 1.6 M ammonium sulfate, 0.1 M MES, pH 6.0. , VAPOR DIFFUSION, SITTING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
10.8 M ammonium sulfate11
20.05 M MES11
31.6 M ammonium sulfate12
40.1 M MES12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9199 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 1.1→42.45 Å / Num. all: 48767 / Num. obs: 45791 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.239 / Num. unique all: 4414 / % possible all: 90.7

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Processing

Software
NameClassification
HKL-2000data collection
EPMRphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model of Native A-RNA

Resolution: 1.1→10 Å / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.142 2152 -RANDOM
Rwork0.108 ---
all0.114 45752 --
obs0.11 43113 94.2 %-
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1016 0 324 1340
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.014
X-RAY DIFFRACTIONs_angle_d0.029

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