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- PDB-6c64: Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO... -

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Basic information

Entry
Database: PDB / ID: 6c64
TitleCrystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3-Biotin
Components
  • RNA (32-MER)
  • RNA (36-MER)
KeywordsRNA / Fluorescent / Aptamer / G-quadruplex
Function / homologyChem-EKM / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.00014879601 Å
AuthorsTrachman, R.J. / Ferre-D'Amare, A.R.
CitationJournal: Biochemistry / Year: 2018
Title: Crystal Structures of the Mango-II RNA Aptamer Reveal Heterogeneous Fluorophore Binding and Guide Engineering of Variants with Improved Selectivity and Brightness.
Authors: Trachman 3rd., R.J. / Abdolahzadeh, A. / Andreoni, A. / Cojocaru, R. / Knutson, J.R. / Ryckelynck, M. / Unrau, P.J. / Ferre-D'Amare, A.R.
History
DepositionJan 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (36-MER)
B: RNA (36-MER)
D: RNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,48613
Polymers34,5083
Non-polymers97810
Water00
1
A: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3865
Polymers11,9361
Non-polymers4504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3865
Polymers11,9361
Non-polymers4504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: RNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7143
Polymers10,6361
Non-polymers782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.098, 181.764, 108.289
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-104-

K

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Components

#1: RNA chain RNA (36-MER)


Mass: 11936.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA was in vitro transcribed / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (32-MER)


Mass: 10635.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA was in vitro transcribed / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EKM / 1-methyl-4-[(1E)-3-(3-methyl-1,3-benzothiazol-3-ium-2-yl)prop-1-en-1-yl]quinolin-1-ium


Mass: 332.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20N2S
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K

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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: 2.65 Å3/Da / Density % sol: 53.5 % / Description: cubic
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 2.45 M Ammonium Formate, 12.5% glycerol, 3% sorbitol
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3→46.52 Å / Num. obs: 7735 / % possible obs: 99.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 58.7167495741 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 4.3
Reflection shellResolution: 3→3.19 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1268 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C63

6c63


Resolution: 3.00014879601→46.5151662692 Å / SU ML: 0.359376037971 / Cross valid method: FREE R-VALUE / σ(F): 1.34562114754 / Phase error: 23.9164508394
RfactorNum. reflection% reflectionSelection details
Rfree0.255076205615 776 10.0323206206 %random selection
Rwork0.189856262024 ---
obs0.196349464513 7735 99.7421018698 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57.3830391657 Å2
Refinement stepCycle: LAST / Resolution: 3.00014879601→46.5151662692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2281 56 0 2337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005759842449032624
X-RAY DIFFRACTIONf_angle_d1.199615704624096
X-RAY DIFFRACTIONf_chiral_restr0.0538579029803518
X-RAY DIFFRACTIONf_plane_restr0.00710507899163108
X-RAY DIFFRACTIONf_dihedral_angle_d21.52443447091241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.18810.2702425817741280.2394996414261140X-RAY DIFFRACTION99.6855345912
3.1881-3.43420.2861322668411260.1905329436481131X-RAY DIFFRACTION99.5249406176
3.4342-3.77960.2682698036931260.2054915695231130X-RAY DIFFRACTION99.3670886076
3.7796-4.32620.2548744542291280.1991181169021150X-RAY DIFFRACTION100
4.3262-5.44920.236301716241310.1851676126181174X-RAY DIFFRACTION100
5.4492-46.52070.2474428578641370.1697246153261234X-RAY DIFFRACTION99.8543335761

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