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- PDB-4qln: structure of ydao riboswitch binding with c-di-dAMP -

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Basic information

Entry
Database: PDB / ID: 4qln
Titlestructure of ydao riboswitch binding with c-di-dAMP
ComponentsRNA (117-MER)
KeywordsRNA / ydao riboswitch / c-di-AMP
Function / homologyChem-2BA / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsRen, A.M. / Patel, D.J.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets.
Authors: Ren, A. / Patel, D.J.
History
DepositionJun 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (117-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8805
Polymers40,5141
Non-polymers1,3654
Water1267
1
A: RNA (117-MER)
hetero molecules

A: RNA (117-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,75910
Polymers81,0282
Non-polymers2,7318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2480 Å2
ΔGint-64 kcal/mol
Surface area35940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.874, 87.051, 144.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsAUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Components

#1: RNA chain RNA (117-MER)


Mass: 40514.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ydao riboswitch
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4 / Description: In vitro translation
#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 293 K
Details: 0.1 M Na-Bicine, pH 8.7-9.2 and 2.6-3.2 M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 8.7-9.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 49287 / % possible obs: 1 % / Observed criterion σ(I): 1.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→45.25 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 33.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.29 732 5.04 %
Rwork0.217 --
obs0.221 13780 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2514 86 7 2607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153035
X-RAY DIFFRACTIONf_angle_d1.824716
X-RAY DIFFRACTIONf_dihedral_angle_d24.3971512
X-RAY DIFFRACTIONf_chiral_restr0.166610
X-RAY DIFFRACTIONf_plane_restr0.011131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.85460.44831360.37572690X-RAY DIFFRACTION99
2.8546-3.14180.36551730.30272718X-RAY DIFFRACTION100
3.1418-3.59630.30421430.22082754X-RAY DIFFRACTION100
3.5963-4.53030.28581390.19962786X-RAY DIFFRACTION100
4.5303-45.2610.24481410.18972840X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -6.9183 Å / Origin y: -31.8936 Å / Origin z: -17.7985 Å
111213212223313233
T0.4516 Å20.0145 Å20.057 Å2-0.4263 Å20.0956 Å2--0.4708 Å2
L4.8849 °2-0.5238 °2-0.9218 °2-1.2601 °20.597 °2--3.4231 °2
S-0.1206 Å °-0.6265 Å °-0.3052 Å °0.0753 Å °-0.0594 Å °0.0341 Å °0.0892 Å °0.0052 Å °0.1386 Å °
Refinement TLS groupSelection details: all

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