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- PDB-6e8t: Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin -

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Basic information

Entry
Database: PDB / ID: 6e8t
TitleStructure of the Mango-III (A10U) aptamer bound to TO1-Biotin
ComponentsRNA (35-MER)
KeywordsRNA / Aptamer / fluorescence / G-quadruplex
Function / homologyChem-HZG / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTrachman, R.J. / Ferre-D'Amare, A.R.
CitationJournal: Nat. Chem. Biol. / Year: 2019
Title: Structure and functional reselection of the Mango-III fluorogenic RNA aptamer.
Authors: Trachman 3rd., R.J. / Autour, A. / Jeng, S.C.Y. / Abdolahzadeh, A. / Andreoni, A. / Cojocaru, R. / Garipov, R. / Dolgosheina, E.V. / Knutson, J.R. / Ryckelynck, M. / Unrau, P.J. / Ferre-D'Amare, A.R.
History
DepositionJul 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: RNA (35-MER)
C: RNA (35-MER)
B: RNA (35-MER)
A: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,17313
Polymers46,6004
Non-polymers1,5739
Water724
1
D: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0373
Polymers11,6501
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0604
Polymers11,6501
Non-polymers4113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0373
Polymers11,6501
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0373
Polymers11,6501
Non-polymers3882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.945, 91.945, 161.691
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11C-103-

NA

21C-201-

HOH

31C-202-

HOH

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Components

#1: RNA chain
RNA (35-MER) / Mango-III (A10U) aptamer


Mass: 11649.898 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-HZG / 1-methyl-4-{[3-(2-oxopropyl)-1,3-benzothiazol-3-ium-2-yl]methyl}quinolin-1-ium


Mass: 348.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H20N2OS
#3: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.6 M Ammonium Citrate, 3.0% Glycerol, 4% Acetone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.105 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105 Å / Relative weight: 1
ReflectionResolution: 2.9→45.97 Å / Num. obs: 18895 / % possible obs: 98.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 77.73 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 10.3
Reflection shellResolution: 2.9→3.03 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.91 / Num. unique obs: 1235 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E8S

6e8s


Resolution: 2.9→45.97 Å / SU ML: 0.5907 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.2373
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1873 5 %random
Rwork0.1945 ---
obs0.1988 18895 83.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 78.05 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3060 105 4 3169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633537
X-RAY DIFFRACTIONf_angle_d1.36965494
X-RAY DIFFRACTIONf_chiral_restr0.0583710
X-RAY DIFFRACTIONf_plane_restr0.007155
X-RAY DIFFRACTIONf_dihedral_angle_d19.52141711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.980.49681390.45061235X-RAY DIFFRACTION79.88
2.98-3.070.4521500.39031340X-RAY DIFFRACTION84.56
3.07-3.170.39011520.33821323X-RAY DIFFRACTION84.38
3.17-3.280.31071320.28451301X-RAY DIFFRACTION82.64
3.28-3.410.27171320.2431212X-RAY DIFFRACTION78.41
3.41-3.570.2831380.24551255X-RAY DIFFRACTION81.65
3.57-3.750.29231560.24021322X-RAY DIFFRACTION83.98
3.75-3.990.31751500.23111377X-RAY DIFFRACTION86.47
3.99-4.30.25251530.19691341X-RAY DIFFRACTION86.46
4.3-4.730.20791350.16911258X-RAY DIFFRACTION81.08
4.73-5.410.21491400.14971402X-RAY DIFFRACTION87.51
5.41-6.810.18011420.14521306X-RAY DIFFRACTION84.28
6.81-45.980.1481540.12971350X-RAY DIFFRACTION86.34

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