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- PDB-2q1r: Crystal Structure Analysis of the RNA Dodecamer CGCGAAUUAGCG, wit... -

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Basic information

Entry
Database: PDB / ID: 2q1r
TitleCrystal Structure Analysis of the RNA Dodecamer CGCGAAUUAGCG, with a G-A mismatch.
ComponentsRNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*AP*GP*CP*G)-3')
KeywordsRNA / G-A mismatch / RNAi
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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*GP*AP*AP*UP*UP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9003
Polymers3,8511
Non-polymers492
Water1,35175
1
A: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*AP*GP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)7,8006
Polymers7,7032
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Unit cell
Length a, b, c (Å)41.339, 34.886, 32.118
Angle α, β, γ (deg.)90.00, 129.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-9033-

HOH

DetailsThe biological assembly is a duplex and correspnds to the crystallographic asymmetric unit, hence no symmetry operators are needed

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Components

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


Mass: 3851.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chemically synthesized
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Droplets containing 0.5 mM oligonucleotide, 5% MPD, 20 mM sodium cacodylate, pH 7.0, 6 mM spermine-4HCl, 40 mM sodium chloride and 10 mM magnesium chloride were equilibrated against a ...Details: Droplets containing 0.5 mM oligonucleotide, 5% MPD, 20 mM sodium cacodylate, pH 7.0, 6 mM spermine-4HCl, 40 mM sodium chloride and 10 mM magnesium chloride were equilibrated against a reservoir of 35% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
15% MPD11
2sodium cacodylate11
3spermine-4HCl11
4sodium chloride11
5magnesium chloride11
635% MPD12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.12→24.84 Å / Num. all: 13446 / Num. obs: 13280 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.035
Reflection shellResolution: 1.12→1.16 Å / Rmerge(I) obs: 0.277 / Num. unique all: 1330 / % possible all: 89.3

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Processing

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

Resolution: 1.12→10 Å / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.182 630 -random
Rwork0.142 ---
all0.149 13514 --
obs0.144 12597 93.2 %-
Refinement stepCycle: LAST / Resolution: 1.12→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 255 2 75 332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_bond_d0.014

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