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- PDB-3p4b: Alternatingly modified 2'Fluoro RNA octamer f/rA2U2-P3 -

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Basic information

Entry
Database: PDB / ID: 3p4b
TitleAlternatingly modified 2'Fluoro RNA octamer f/rA2U2-P3
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 / homology: / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.2Sep 6, 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 / pdbx_struct_special_symmetry / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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: 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'
C: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
D: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
E: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
F: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4828
Polymers15,2076
Non-polymers2752
Water2,540141
1
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)5,2063
Polymers5,0692
Non-polymers1371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
D: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2063
Polymers5,0692
Non-polymers1371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
F: 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'


Theoretical massNumber of molelcules
Total (without water)5,0692
Polymers5,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.383, 43.383, 60.987
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
11A-803-

HOH

21B-769-

HOH

31B-822-

HOH

41C-743-

HOH

51C-744-

HOH

61F-831-

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.: 6 / Source method: obtained synthetically / Details: Chemically synthesized modified RNA octamer
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium cacodylate (40 mM, pH 6.0), sodium chloride (80 mM), barium chloride (20 mM), spermine tetrahydrochloride (12 mM), and 2-methyl-2,4-pentanediol (MPD; 10% (v/v)), equilibrated against ...Details: Sodium cacodylate (40 mM, pH 6.0), sodium chloride (80 mM), barium chloride (20 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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 22793 / Num. obs: 21294 / % possible obs: 98.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 39
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.34 / Num. unique all: 1005 / % possible all: 81.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P4A

3p4a


Resolution: 1.45→21.69 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.288 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25083 1141 5.1 %RANDOM
Rwork0.1971 ---
obs0.19962 21294 100 %-
all-22442 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.807 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.45→21.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1002 2 141 1145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211096
X-RAY DIFFRACTIONr_angle_refined_deg2.07731692
X-RAY DIFFRACTIONr_chiral_restr0.1150.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02490
X-RAY DIFFRACTIONr_scbond_it4.15331096
X-RAY DIFFRACTIONr_scangle_it4.9664.51692
X-RAY DIFFRACTIONr_rigid_bond_restr3.50331096
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 68 -
Rwork0.293 1343 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0840.0666-1.03593.1172-0.52050.85090.01450.0404-0.165-0.22320.03670.18270.05690.0611-0.05120.05130.0074-0.02420.0441-0.03710.0491-0.61614.00120.5898
21.2227-0.09571.19263.3141-0.57881.22680.0193-0.05290.19280.2360.05670.2027-0.06140.0911-0.0760.0474-0.00580.02720.0444-0.0430.0551-0.841710.9764-21.0515
30.9392-0.0895-0.06233.35971.310.170.24810.00610.00390.0106-0.1537-0.2427-0.0041-0.1091-0.09440.05310.00110.00110.02380.00140.06567.951412.546320.3729
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A - X101 - 108
2X-RAY DIFFRACTION1A - X201 - 208
3X-RAY DIFFRACTION2A - X301 - 308
4X-RAY DIFFRACTION2A - X401 - 408
5X-RAY DIFFRACTION3A - X501 - 508
6X-RAY DIFFRACTION3A - X601 - 608

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