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- PDB-6c63: Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO... -

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Basic information

Entry
Database: PDB / ID: 6c63
TitleCrystal Structure of the Mango-II Fluorescent Aptamer Bound to TO1-Biotin
Components
  • RNA (32-MER)
  • RNA (36-MER)
KeywordsRNA / fluorescent / aptamer / G-quadruplex
Function / homologyChem-EKJ / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.90002801531 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_asym_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)
C: RNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,04314
Polymers34,5083
Non-polymers1,53511
Water00
1
A: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4615
Polymers11,9361
Non-polymers5254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4224
Polymers11,9361
Non-polymers4863
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1605
Polymers10,6361
Non-polymers5254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.831, 182.412, 107.494
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 prepared by in vitro transcription / 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 prepared by in vitro transcription / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EKJ / 4-[(3-{2-[(2-methoxyethyl)amino]-2-oxoethyl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium


Mass: 407.529 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H25N3O2S
#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: 2.61 Å3/Da / Density % sol: 52.94 %
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, 14.5% glycerol, 6.5% D-Sorbitol
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.495 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.495 Å / Relative weight: 1
ReflectionResolution: 2.9→91.206 Å / Num. obs: 15464 / % possible obs: 99 % / Redundancy: 8.8 % / Biso Wilson estimate: 74.48313766 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 4.4
Reflection shellResolution: 2.9→2.99 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.34 / Num. unique obs: 1257 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V3F

5v3f


Resolution: 2.90002801531→91.206 Å / Rfactor Rfree error: 0.01 / SU ML: 0.30161926081 / Cross valid method: FREE R-VALUE / σ(F): 1.34361859768 / Phase error: 24.2447936435
RfactorNum. reflection% reflectionSelection details
Rfree0.229552478319 1530 9.89394723228 %10%
Rwork0.185091842879 ---
obs0.189598873662 15464 99.6455957214 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 76.7561539806 Å2
Refinement stepCycle: LAST / Resolution: 2.90002801531→91.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2281 95 0 2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006540424548172666
X-RAY DIFFRACTIONf_angle_d1.370248044884152
X-RAY DIFFRACTIONf_chiral_restr0.0541752524783518
X-RAY DIFFRACTIONf_plane_restr0.00741684630867111
X-RAY DIFFRACTIONf_dihedral_angle_d22.57805569971256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.99360.2528368600441370.2281005510361257X-RAY DIFFRACTION100
2.9936-3.10060.3489663191921450.2271568363731293X-RAY DIFFRACTION100
3.1006-3.22480.2946370156141390.1956096909161252X-RAY DIFFRACTION99.7847919656
3.2248-3.37160.2336281455381450.1828454930861267X-RAY DIFFRACTION99.366643209
3.3716-3.54930.2670507796981390.1840007534231246X-RAY DIFFRACTION99.3543758967
3.5493-3.77170.2467863331811380.1960387284131257X-RAY DIFFRACTION98.7960339943
3.7717-4.06290.1999845346661390.1843078116221295X-RAY DIFFRACTION99.9303135889
4.0629-4.47180.2550181022291350.1900187644881254X-RAY DIFFRACTION99.7844827586
4.4718-5.11880.233075291431360.1824976613871272X-RAY DIFFRACTION99.8581560284
5.1188-6.44890.1758370634941400.155541233311258X-RAY DIFFRACTION99.5726495726
6.4489-91.25110.2184033673281370.1912686137641283X-RAY DIFFRACTION99.7891777934

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