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- PDB-3p4c: Alternatingly modified 2'Fluoro RNA octamer f/rA2U2-R32 -

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Basic information

Entry
Database: PDB / ID: 3p4c
TitleAlternatingly modified 2'Fluoro RNA octamer f/rA2U2-R32
Components5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
KeywordsRNA / 2'-FLUORO-RNA O2'-MODIFICATION / OCTAMER / 2'-fluoro 2'-deoxycytidine / 2'-fluoro 2'-deoxyadenosine / 2'-fluoro 2'-deoxyuridine / siRNA
Function / homologySTRONTIUM ION / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsPallan, P.S. / Greene, E.M. / Jicman, P.A. / Pandey, R.K. / Manoharan, M. / Rozners, E. / 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 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jun 24, 2020Group: Database references / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / struct_conn ...pdbx_entity_src_syn / struct_conn / struct_ref / struct_ref_seq
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_conn.pdbx_leaving_atom_flag
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
B: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3325
Polymers5,0692
Non-polymers2633
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
B: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
hetero molecules

A: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
B: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,66410
Polymers10,1384
Non-polymers5266
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area3920 Å2
ΔGint-146 kcal/mol
Surface area4780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.550, 40.550, 117.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-303-

SR

21A-322-

HOH

31A-343-

HOH

41A-363-

HOH

51A-387-

HOH

61B-328-

HOH

71B-392-

HOH

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Components

#1: RNA chain 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'


Mass: 2534.525 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized modified RNA / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SR / STRONTIUM ION / Strontium


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


Mass: 18.015 Da / Num. of mol.: 93 / 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: 1.83 Å3/Da / Density % sol: 32.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium cacodylate (40 mM, pH 6.0), lithium chloride (40 mM), strontium chloride (80 mM), spermine tetrahydrochloride (12 mM), and 2-methyl-2,4-pentanediol (MPD; 10% (v/v)), equilibrated ...Details: Sodium cacodylate (40 mM, pH 6.0), lithium chloride (40 mM), strontium chloride (80 mM), spermine tetrahydrochloride (12 mM), and 2-methyl-2,4-pentanediol (MPD; 10% (v/v)), equilibrated against a reservoir of MPD (1 mL, 35%) , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.7687 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2008
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7687 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. all: 13629 / Num. obs: 13343 / % possible obs: 97.9 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 50.1
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.43 / Num. unique all: 489 / % possible all: 72.9

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Processing

Software
NameClassification
MAR345dtbdata collection
HKL2Mapmodel building
SHELXLrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
SHELXL-97refinement
RefinementMethod to determine structure: SAD / Resolution: 1.15→50 Å / WRfactor Rwork: 0.182 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.249 666 -
Rwork0.182 --
obs0.182 13314 99.8 %
all-13343 -
Refinement stepCycle: LAST / Resolution: 1.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 334 3 93 430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.027

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