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- PDB-6e80: Crystal structure of the Corn aptamer in unliganded state -

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Basic information

Entry
Database: PDB / ID: 6.0E+80
TitleCrystal structure of the Corn aptamer in unliganded state
ComponentsRNA (36-MER)
KeywordsRNA / polyribonucleotide / fluorigenic aptamer / G-quadruplex / apo
Function / homologyACETATE ION / : / IRIDIUM HEXAMMINE ION / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.901 Å
AuthorsSjekloca, L. / Ferre-D'Amare, A.R.
CitationJournal: Cell Chem Biol / Year: 2019
Title: Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence.
Authors: Sjekloca, L. / Ferre-D'Amare, A.R.
History
DepositionJul 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,31613
Polymers11,7941
Non-polymers1,52212
Water362
1
A: RNA (36-MER)
hetero molecules

A: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,63226
Polymers23,5882
Non-polymers3,04424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Unit cell
Length a, b, c (Å)93.012, 93.012, 66.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-112-

IR

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (36-MER)


Mass: 11794.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 14 molecules

#2: Chemical ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H18IrN6
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ir
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.42 Å3/Da / Density % sol: 49.17 % / Description: rectangular plate-shaped
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 4000, 0.2 M ammonium acetate pH 6.7, sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.10503 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10503 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 3961 / % possible obs: 89.2 % / Redundancy: 2.1 % / Biso Wilson estimate: 52.61 Å2 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.109 / Rrim(I) all: 0.184 / Χ2: 5.001 / Net I/σ(I): 8.4 / Num. measured all: 8472
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.441.30.4551340.7390.4550.6440.60463.5
2.44-2.491.40.5261550.5850.5210.7410.68269.8
2.49-2.531.50.5141850.5170.4840.7080.73580.4
2.53-2.591.80.7071650.1450.580.9190.72280.5
2.59-2.641.70.771860.5110.6291.0010.984.9
2.64-2.71.90.4741800.7120.3720.6060.77784.5
2.7-2.771.80.4841990.6980.4080.6370.83885.4
2.77-2.851.90.441900.8110.3530.5670.95393.1
2.85-2.9320.4172110.7360.3340.5370.79992.1
2.93-3.022.40.3562120.8470.2510.4381.23494.6
3.02-3.132.40.2422070.8840.1770.3022.24896.7
3.13-3.262.40.2312120.9540.1590.2812.75696.8
3.26-3.412.50.1712070.9720.1270.2142.78992.4
3.41-3.582.30.1482140.9730.1120.1862.85396
3.58-3.812.30.142120.9570.1040.1753.46797.2
3.81-4.12.50.1352270.9340.0990.1684.90597.8
4.1-4.522.50.1122120.9720.0820.144.88295.9
4.52-5.172.40.0932140.9780.0710.1185.61495.1
5.17-6.512.50.0932200.9720.0690.1168.26794.8
6.51-502.40.142190.9380.10.17330.37789.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å46.51 Å
Translation2.4 Å46.51 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 6.0E+81 / Resolution: 2.901→46.506 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 33.34
RfactorNum. reflection% reflection
Rfree0.3071 401 9.86 %
Rwork0.2524 --
obs0.2575 4068 85.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.92 Å2 / Biso mean: 48.8336 Å2 / Biso min: 25.55 Å2
Refinement stepCycle: final / Resolution: 2.901→46.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 762 36 2 800
Biso mean--61.16 38.04 -
Num. residues----35
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001878
X-RAY DIFFRACTIONf_angle_d0.2921384
X-RAY DIFFRACTIONf_chiral_restr0.019175
X-RAY DIFFRACTIONf_plane_restr0.00237
X-RAY DIFFRACTIONf_dihedral_angle_d12.365417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9009-3.32050.3051360.25051208134485
3.3205-4.18310.27051350.24611212134785
4.1831-46.5120.33371300.25721247137786
Refinement TLS params.Method: refined / Origin x: 15.1918 Å / Origin y: 60.3891 Å / Origin z: 26.9675 Å
111213212223313233
T0.2789 Å2-0.0437 Å20.0145 Å2-0.453 Å2-0.0732 Å2--0.3376 Å2
L2.874 °20.8669 °2-0.1169 °2-2.7529 °2-2.6408 °2--3.6548 °2
S0.0255 Å °-0.6737 Å °0.1916 Å °-0.0286 Å °-0.1524 Å °-0.0385 Å °0.2144 Å °0.3927 Å °0.3963 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 36
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allC2 - 3
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allE1 - 5
6X-RAY DIFFRACTION1allE6
7X-RAY DIFFRACTION1allF2 - 3
8X-RAY DIFFRACTION1allG1
9X-RAY DIFFRACTION1allG2
10X-RAY DIFFRACTION1allI1
11X-RAY DIFFRACTION1allI2

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