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- PDB-6c65: Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound ... -

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Basic information

Entry
Database: PDB / ID: 6c65
TitleCrystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin
Components
  • RNA (35-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: 2.8000516274 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 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)
C: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,97014
Polymers35,4353
Non-polymers1,53511
Water00
1
A: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4385
Polymers11,9131
Non-polymers5254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4385
Polymers11,9131
Non-polymers5254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0944
Polymers11,6081
Non-polymers4863
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.639, 179.680, 108.313
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: 11913.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA was in vitro transcribed / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (35-MER)


Mass: 11608.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA was in vitro transcribed / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 10mM NiCl2, 2.3M Ammonium Formate, 12% glycerol
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.722 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.722 Å / Relative weight: 1
ReflectionResolution: 2.8→46.3812063611 Å / Num. obs: 9216 / % possible obs: 99.8 % / Redundancy: 11.3 % / Biso Wilson estimate: 58.2741228221 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 3.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.956 / Num. unique obs: 1254 / % 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 / Resolution: 2.8000516274→46.3812063611 Å / SU ML: 0.373640648423 / Cross valid method: FREE R-VALUE / σ(F): 1.34284986911 / Phase error: 25.149206905
RfactorNum. reflection% reflectionSelection details
Rfree0.236886262215 923 10.0151909722 %Random selection
Rwork0.185884901444 ---
obs0.191169345205 9216 99.761853215 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.7768970597 Å2
Refinement stepCycle: LAST / Resolution: 2.8000516274→46.3812063611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2339 95 0 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007079335161152730
X-RAY DIFFRACTIONf_angle_d1.224747810384250
X-RAY DIFFRACTIONf_chiral_restr0.0549304903207528
X-RAY DIFFRACTIONf_plane_restr0.00709617966163115
X-RAY DIFFRACTIONf_dihedral_angle_d19.73468229091283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.94770.3120164903281250.295808781791129X-RAY DIFFRACTION99.5238095238
2.9477-3.13230.2913579592281310.2490287002371176X-RAY DIFFRACTION99.9235474006
3.1323-3.37410.2528475706381300.1835359284131167X-RAY DIFFRACTION99.6159754224
3.3741-3.71350.2638035306541300.199267985531159X-RAY DIFFRACTION99.3831919815
3.7135-4.25050.2581471342921300.191268077911181X-RAY DIFFRACTION100
4.2505-5.35390.2146517146461340.1800744596781203X-RAY DIFFRACTION100
5.3539-46.38750.1936544195721430.149186620261278X-RAY DIFFRACTION99.8594518623

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