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- PDB-3p4a: 2'Fluoro modified RNA octamer fA2U2 -

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Basic information

Entry
Database: PDB / ID: 3p4a
Title2'Fluoro modified RNA octamer fA2U2
Components2'Fluoro modified RNA 8-MER
KeywordsRNA / 2'-FLUORO-RNA / O2'-MODIFICATION / OCTAMER / 2'-fluoro 2'-deoxycytidine / 2'-fluoro 2'-deoxyguanosine / 2'-fluoro 2'-deoxyadenosine / 2'-fluoro 2'-deoxyuridine / siRNA
Function / homologySTRONTIUM ION / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsManoharan, M. / Akinc, A. / Pandey, R.K. / Qin, J. / Hadwiger, P. / John, M. / Mills, K. / Charisse, K. / Maier, M.A. / Nechev, L. ...Manoharan, M. / Akinc, A. / Pandey, R.K. / Qin, J. / Hadwiger, P. / John, M. / Mills, K. / Charisse, K. / Maier, M.A. / Nechev, L. / Greene, E.M. / Pallan, P.S. / Rozners, E. / Rajeev, K.G. / Egli, M.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA.
Authors: Pallan, P.S. / Greene, E.M. / Jicman, P.A. / Pandey, R.K. / Manoharan, M. / Rozners, E. / Egli, M.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 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_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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: 2'Fluoro modified RNA 8-MER
B: 2'Fluoro modified RNA 8-MER
C: 2'Fluoro modified RNA 8-MER
D: 2'Fluoro modified RNA 8-MER
E: 2'Fluoro modified RNA 8-MER
F: 2'Fluoro modified RNA 8-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,09217
Polymers15,2556
Non-polymers83711
Water5,332296
1
A: 2'Fluoro modified RNA 8-MER
B: 2'Fluoro modified RNA 8-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2855
Polymers5,0852
Non-polymers2003
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 2'Fluoro modified RNA 8-MER
D: 2'Fluoro modified RNA 8-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4356
Polymers5,0852
Non-polymers3504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 2'Fluoro modified RNA 8-MER
F: 2'Fluoro modified RNA 8-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3726
Polymers5,0852
Non-polymers2874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.245, 43.245, 60.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11B-711-

MG

21E-712-

MG

31A-859-

HOH

41B-723-

HOH

51B-736-

HOH

61B-828-

HOH

71B-871-

HOH

81B-896-

HOH

91B-929-

HOH

101C-729-

HOH

111C-740-

HOH

121D-717-

HOH

131D-743-

HOH

141E-710-

HOH

151E-735-

HOH

161E-987-

HOH

171E-989-

HOH

181E-1004-

HOH

191F-727-

HOH

201F-943-

HOH

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Components

#1: RNA chain
2'Fluoro modified RNA 8-MER


Mass: 2542.489 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Chemically synthesized modified RNA
#2: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40mM Sodium cacodylate pH 6.0, 80 mM strontium chloride, 20 mM magnesium chloride, 12mM spermine tetrahydrochloride, 10% 2-methyl-2,4-pentanediol, equilibrated against a reservoir of 35% ...Details: 40mM Sodium cacodylate pH 6.0, 80 mM strontium chloride, 20 mM magnesium chloride, 12mM spermine tetrahydrochloride, 10% 2-methyl-2,4-pentanediol, equilibrated against a reservoir of 35% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-D10.7689
SYNCHROTRONAPS 21-ID-D20.9787
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDNov 17, 2008
MARMOSAIC 300 mm CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.76891
20.97871
ReflectionResolution: 1.2→30 Å / Num. all: 40060 / Num. obs: 39940 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 38.8
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4027 / % possible all: 99.3

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Processing

Software
NameClassification
MAR345dtbdata collection
HKL2Mapmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→30 Å / Cross valid method: Troughout / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1997 -Random
Rwork0.17 ---
obs0.17 39888 99.9 %-
all-39940 --
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1002 11 296 1309
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.026
LS refinement shellResolution: 1.2→1.24 Å

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