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- PDB-5ob3: iSpinach aptamer -

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Basic information

Entry
Database: PDB / ID: 5ob3
TitleiSpinach aptamer
ComponentsRNA aptamer (69-MER)
KeywordsRNA / aptamer / iSpinach / DFHBI
Function / homologyChem-1TU / : / SPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsFernandez-Millan, P. / Autour, A. / Westhof, E. / Ryckelynck, M.
CitationJournal: RNA / Year: 2017
Title: Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI.
Authors: Fernandez-Millan, P. / Autour, A. / Ennifar, E. / Westhof, E. / Ryckelynck, M.
History
DepositionJun 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA aptamer (69-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9085
Polymers22,3731
Non-polymers5354
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint1 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.700, 48.500, 30.100
Angle α, β, γ (deg.)90.000, 91.860, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

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Components

#1: RNA chain RNA aptamer (69-MER)


Mass: 22373.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-1TU / 4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol


Mass: 254.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12F2N2O2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 40 mM NaCl, 40 mM Sodium cacodylate pH 7.0, 32% MPD, 12 mM Spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.80002 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.80002 Å / Relative weight: 1
ReflectionResolution: 2.004→46.17 Å / Num. obs: 27458 / % possible obs: 99 % / Redundancy: 15.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.106 / Net I/σ(I): 17.6
Reflection shellResolution: 2.004→2.12 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2470 / CC1/2: 0.82 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4q9r.pdb

4q9r


Resolution: 2.004→46.166 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.47
RfactorNum. reflection% reflection
Rfree0.2226 1406 5.12 %
Rwork0.1983 --
obs0.1996 27458 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.08 Å2 / Biso mean: 62.5115 Å2 / Biso min: 22.68 Å2
Refinement stepCycle: final / Resolution: 2.004→46.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1483 46 51 1580
Biso mean--43.53 43.06 -
Num. residues----69
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061690
X-RAY DIFFRACTIONf_angle_d1.1872626
X-RAY DIFFRACTIONf_chiral_restr0.05345
X-RAY DIFFRACTIONf_plane_restr0.00771
X-RAY DIFFRACTIONf_dihedral_angle_d17.705838
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.004-2.07570.29331030.35071700180364
2.0757-2.15880.31751260.27232674280097
2.1588-2.2570.29541360.236627102846100
2.257-2.3760.28791530.240426942847100
2.376-2.52490.29731580.223327052863100
2.5249-2.71980.28421450.25127482893100
2.7198-2.99340.3191400.253627162856100
2.9934-3.42650.24641160.210527082824100
3.4265-4.31650.18131570.175427082865100
4.3165-46.17790.17151720.147926892861100
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)
15.19660.3344-3.42411.98851.54954.34590.064-0.355-0.25540.8133-0.22860.7171-0.3712-1.26120.15050.75850.23910.20140.89120.04290.7769-57.22212.17279.1736
25.1115-0.3596-0.36532.5087-0.36672.2406-0.10060.27910.2924-0.0423-0.0471-0.45830.16840.52680.05990.31890.0012-0.01680.38730.04780.3115-24.505314.5684-8.6073
39.65290.35554.97081.90950.16322.94360.51310.06190.0921-0.0757-0.3551-0.80240.3690.3110.12010.39150.013-0.02930.58170.0120.6294-11.119514.7252-7.898
42.39560.6707-1.24484.16090.07112.5731-0.1004-0.0255-0.23070.44880.1143-0.14070.24220.21140.09160.30460.021-0.03390.2185-0.00880.2326-33.1967.1393-3.223
52.95861.5213-1.05331.89361.19143.0953-0.2235-0.62710.19960.67680.10560.8894-0.2908-1.0601-0.03120.60430.16150.20180.90220.06140.7016-59.480514.889411.2808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 13 )A1 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 30 )A14 - 30
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 42 )A31 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 56 )A43 - 56
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 69 )A57 - 69

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