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- PDB-6v9d: Co-crystal structure of the fluorogenic Mango-IV homodimer bound ... -

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Basic information

Entry
Database: PDB / ID: 6v9d
TitleCo-crystal structure of the fluorogenic Mango-IV homodimer bound to TO1-Biotin
ComponentsRNA (28-MER)
KeywordsRNA / aptamer / fluorescence
Function / homologyBROMIDE ION / : / Chem-QW4 / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsTrachman, R.J. / Ferre-D'Amare, A.R.
CitationJournal: Structure / Year: 2020
Title: Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields an RNA FRET Pair.
Authors: Trachman 3rd, R.J. / Cojocaru, R. / Wu, D. / Piszczek, G. / Ryckelynck, M. / Unrau, P.J. / Ferre-D'Amare, A.R.
History
DepositionDec 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 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

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Assembly

Deposited unit
B: RNA (28-MER)
E: RNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,82611
Polymers18,4672
Non-polymers1,3599
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Constant Velocity AUC Size exclusion chromotography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint7 kcal/mol
Surface area9700 Å2
Unit cell
Length a, b, c (Å)48.917, 48.917, 122.972
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: RNA chain RNA (28-MER)


Mass: 9233.559 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-QW4 / 2-[(E)-(1-methylquinolin-4(1H)-ylidene)methyl]-3-(2-oxopropyl)-1,3-benzothiazol-3-ium


Mass: 347.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H19N2OS
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.01 M CoCl2, 1.65-1.75 M NH4SO4, 0.01-0.015 M Phenol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.64→42.36 Å / Num. obs: 8121 / % possible obs: 99.6 % / Redundancy: 16.2 % / Biso Wilson estimate: 53.86 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.093 / Net I/σ(I): 15.8
Reflection shellResolution: 2.64→2.71 Å / Rmerge(I) obs: 1.06 / Num. unique obs: 1214 / CC1/2: 0.41

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→42.36 Å / SU ML: 0.3897 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0625
RfactorNum. reflection% reflection
Rfree0.2722 815 10.04 %
Rwork0.2196 --
obs0.2252 8121 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.77 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1206 81 0 1287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681440
X-RAY DIFFRACTIONf_angle_d1.46552240
X-RAY DIFFRACTIONf_chiral_restr0.0791273
X-RAY DIFFRACTIONf_plane_restr0.007964
X-RAY DIFFRACTIONf_dihedral_angle_d25.7129664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.980.37521370.3281214X-RAY DIFFRACTION99.78
2.98-3.210.34231240.25141239X-RAY DIFFRACTION99.93
3.21-3.530.2611470.20881203X-RAY DIFFRACTION99.85
3.53-4.040.28161490.21821215X-RAY DIFFRACTION99.93
4.04-5.090.25441270.20421203X-RAY DIFFRACTION100
5.09-42.360.23731310.20151232X-RAY DIFFRACTION99.93

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