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- PDB-7l0z: Spinach variant bound to DFHBI-1T -

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Basic information

Entry
Database: PDB / ID: 7l0z
TitleSpinach variant bound to DFHBI-1T
ComponentsRNA (69-MER)
KeywordsRNA / fluorescent / aptamer
Function / homologyChem-2ZY / : / PHOSPHATE ION / SPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTruong, L. / Trachman, R.J. / Ferre-D'Amare, A.R.
CitationJournal: Rna / Year: 2021
Title: Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.
Authors: Jeng, S.C.Y. / Trachman III, R.J. / Weissenboeck, F. / Truong, L. / Link, K.A. / Jepsen, M.D.E. / Knutson, J.R. / Andersen, E.S. / Ferre-D'Amare, A.R. / Unrau, P.J.
History
DepositionDec 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
G: RNA (69-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,63912
Polymers22,3731
Non-polymers1,26611
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-44 kcal/mol
Surface area12330 Å2
Unit cell
Length a, b, c (Å)150.564, 48.692, 30.612
Angle α, β, γ (deg.)90.000, 91.364, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11G-105-

MG

21G-109-

NA

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Components

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RNA chain , 1 types, 1 molecules G

#1: RNA chain RNA (69-MER)


Mass: 22373.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 65 molecules

#2: Chemical ChemComp-2ZY / (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one


Mass: 320.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9F5N2O2
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 40 mM Tris-HCl pH 7.5, 100 mM KCl, 1 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.105 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105 Å / Relative weight: 1
ReflectionResolution: 2.01→75.26 Å / Num. obs: 14648 / % possible obs: 98.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 46.31 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.5
Reflection shellResolution: 2.01→2.07 Å / Num. unique obs: 1167 / CC1/2: 0.627 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OB3

5ob3


Resolution: 2.1→75.26 Å / SU ML: 0.2582 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8783
RfactorNum. reflection% reflection
Rfree0.2324 1293 9.98 %
Rwork0.1959 --
obs0.1996 11686 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→75.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1483 75 54 1612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611724
X-RAY DIFFRACTIONf_angle_d1.11822665
X-RAY DIFFRACTIONf_chiral_restr0.0506345
X-RAY DIFFRACTIONf_plane_restr0.006871
X-RAY DIFFRACTIONf_dihedral_angle_d17.2425858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.331460.2991308X-RAY DIFFRACTION98.91
2.18-2.280.28311450.26691259X-RAY DIFFRACTION99.29
2.28-2.40.30281410.25841302X-RAY DIFFRACTION99.18
2.4-2.550.25051470.23741309X-RAY DIFFRACTION98.91
2.55-2.750.2851390.2491267X-RAY DIFFRACTION98.53
2.75-3.030.32231400.26421298X-RAY DIFFRACTION98.97
3.03-3.470.26561380.21041276X-RAY DIFFRACTION97.79
3.47-4.370.20661500.17841322X-RAY DIFFRACTION99.26
4.37-75.260.1721470.13911321X-RAY DIFFRACTION98.19
Refinement TLS params.Method: refined / Origin x: -36.8152928881 Å / Origin y: 12.3705808217 Å / Origin z: -0.479627498632 Å
111213212223313233
T0.420948081066 Å20.0260468795674 Å2-0.0545975283894 Å2-0.236482955583 Å2-0.0149382859037 Å2--0.244261938933 Å2
L5.01072173497 °2-0.150228286574 °2-0.598431720792 °2-2.42095497899 °2-0.280314402507 °2--2.1857530096 °2
S-0.0722560140963 Å °-0.179569026511 Å °0.0709574158993 Å °0.290368139125 Å °0.0897809830997 Å °0.139898891319 Å °0.016607284078 Å °-0.149997906571 Å °-0.00115005845845 Å °
Refinement TLS groupSelection details: all

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