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- PDB-4ts2: Crystal structure of the Spinach RNA aptamer in complex with DFHB... -

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Basic information

Entry
Database: PDB / ID: 4ts2
TitleCrystal structure of the Spinach RNA aptamer in complex with DFHBI, magnesium ions
Components(Spinach aptamer RNA, bimolecular ...) x 2
KeywordsRNA / aptamer / fluorescence / G-quadruplex
Function / homologysucrose / Chem-38E / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.884 Å
AuthorsWarner, K.D. / Chen, M.C. / Song, W. / Strack, R.L. / Thorn, A. / Jaffrey, S.R. / Ferre-D'Amare, A.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural basis for activity of highly efficient RNA mimics of green fluorescent protein.
Authors: Warner, K.D. / Chen, M.C. / Song, W. / Strack, R.L. / Thorn, A. / Jaffrey, S.R. / Ferre-D'Amare, A.R.
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity / pdbx_database_status ...entity / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / refine_hist / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Apr 13, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end
Revision 3.1Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Spinach aptamer RNA, bimolecular construct
Y: Spinach aptamer RNA, bimolecular construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3528
Polymers29,6162
Non-polymers7366
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-39 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.877, 49.399, 188.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Spinach aptamer RNA, bimolecular ... , 2 types, 2 molecules XY

#1: RNA chain Spinach aptamer RNA, bimolecular construct


Mass: 14394.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain Spinach aptamer RNA, bimolecular construct


Mass: 15220.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 1 types, 1 molecules

#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 10 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-38E / (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one


Mass: 252.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10F2N2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.5M NaCl, 0.1M succinate-K pH 7.0, 10% sucrose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 8415 / % possible obs: 99.6 % / Redundancy: 5.1 % / Net I/σ(I): 23.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.884→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 33.018 / SU ML: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.213 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 477 5.4 %RANDOM
Rwork0.2129 8415 --
obs0.2154 8892 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 263.47 Å2 / Biso mean: 108.601 Å2 / Biso min: 54.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å20 Å2
2---2.31 Å20 Å2
3---0.8 Å2
Refinement stepCycle: final / Resolution: 2.884→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1899 68 5 1972
Biso mean--135.28 99.1 -
Num. residues----90
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0112194
X-RAY DIFFRACTIONr_bond_other_d0.0030.02905
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.3453420
X-RAY DIFFRACTIONr_angle_other_deg1.90932197
X-RAY DIFFRACTIONr_chiral_restr0.0960.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021083
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02482
X-RAY DIFFRACTIONr_scbond_it6.0948.3492194
LS refinement shellResolution: 2.884→2.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.562 29 -
Rwork0.468 580 -
all-609 -
obs--99.02 %
Refinement TLS params.Method: refined / Origin x: -18.3214 Å / Origin y: 2.0927 Å / Origin z: -1.3038 Å
111213212223313233
T0.1872 Å20.0011 Å2-0.1456 Å2-0.2896 Å20.0442 Å2--0.3944 Å2
L1.0718 °2-0.5619 °2-0.6191 °2-0.7337 °20.2149 °2--0.9165 °2
S0.2034 Å °-0.1564 Å °-0.296 Å °-0.1055 Å °-0.0009 Å °0.3519 Å °0.0926 Å °0.1414 Å °-0.2025 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 44
2X-RAY DIFFRACTION1Y49 - 95

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