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- PDB-7oa3: Crystal structure of Chili RNA aptamer in complex with DMHBO+ (Ir... -

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Basic information

Entry
Database: PDB / ID: 7oa3
TitleCrystal structure of Chili RNA aptamer in complex with DMHBO+ (Iridium hexammine co-crystallized form)
ComponentsChili RNA Aptamer
KeywordsRNA / RNA aptamer / aptamer / Chili / fluorogenic RNA
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / : / : / DMHBO+ / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsMieczkowski, M. / Pena, V. / Hoebartner, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council (ERC)682586 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine.
Authors: Mieczkowski, M. / Steinmetzger, C. / Bessi, I. / Lenz, A.K. / Schmiedel, A. / Holzapfel, M. / Lambert, C. / Pena, V. / Hobartner, C.
History
DepositionApr 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Chili RNA Aptamer
B: Chili RNA Aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,92717
Polymers33,8642
Non-polymers3,06315
Water00
1
A: Chili RNA Aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5609
Polymers16,9321
Non-polymers1,6288
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chili RNA Aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3688
Polymers16,9321
Non-polymers1,4367
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.605, 54.026, 87.532
Angle α, β, γ (deg.)90.000, 95.494, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 2 through 33 or (resid 34...A2 - 54
221(chain 'B' and (resid 2 through 52 or resid 53 through 58))B2 - 54

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain Chili RNA Aptamer


Mass: 16932.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 15 molecules

#2: Chemical ChemComp-V5Z / DMHBO+ / [4-[(4Z)-4-[(3,5-dimethoxy-4-oxidanyl-phenyl)methylidene]-2-[(Z)-hydroxyiminomethyl]-5-oxidanylidene-imidazol-1-yl]phenyl]-trimethyl-azanium


Mass: 425.458 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ir
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: PEG400, MES , spermine tetrahydrochloride, iridium (III) hexamine
PH range: 5.4 - 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.1035 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 24, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1035 Å / Relative weight: 1
ReflectionResolution: 2.8→45.92 Å / Num. obs: 8215 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 132.08 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.018 / Rrim(I) all: 0.067 / Rsym value: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.95 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1177 / CC1/2: 0.534 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→45.92 Å / SU ML: 0.6033 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 41.8568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2413 783 4.99 %
Rwork0.225 14923 -
obs0.2262 8166 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 155.77 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2170 137 0 2307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152557
X-RAY DIFFRACTIONf_angle_d0.47323984
X-RAY DIFFRACTIONf_chiral_restr0.0208515
X-RAY DIFFRACTIONf_plane_restr0.0017109
X-RAY DIFFRACTIONf_dihedral_angle_d17.05961235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.980.50531280.58442441X-RAY DIFFRACTION96.94
2.98-3.210.40051160.39812499X-RAY DIFFRACTION98.72
3.21-3.530.38141230.32942501X-RAY DIFFRACTION99.47
3.53-4.040.27471400.25672488X-RAY DIFFRACTION99.47
4.04-5.090.24161370.24792492X-RAY DIFFRACTION99.77
5.09-45.920.19731390.17552502X-RAY DIFFRACTION99.85
Refinement TLS params.Method: refined / Origin x: 26.266804016 Å / Origin y: -1.0567545672 Å / Origin z: 9.69210838555 Å
111213212223313233
T1.29566517124 Å20.0724879028518 Å2-0.0706067965462 Å2-1.62766816991 Å20.0294214180278 Å2--1.32746721149 Å2
L2.0477493191 °2-0.613158765364 °2-0.0775412634411 °2-3.02046184615 °2-0.982505443836 °2--1.48066308345 °2
S-0.114915932274 Å °0.294080626874 Å °0.0794136153807 Å °0.519704779046 Å °0.274622965586 Å °0.585350480323 Å °0.193721830238 Å °0.492753812392 Å °-0.235121006668 Å °
Refinement TLS groupSelection details: all

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