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- PDB-4qk9: Thermovirga lienii c-di-AMP riboswitch -

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Basic information

Entry
Database: PDB / ID: 4qk9
TitleThermovirga lienii c-di-AMP riboswitch
ComponentsC-di-AMP riboswitch
KeywordsRNA / c-di-AMP riboswitch
Function / homologyChem-2BA / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsGao, A. / Serganov, A.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Structural insights into recognition of c-di-AMP by the ydaO riboswitch.
Authors: Gao, A. / Serganov, A.
History
DepositionJun 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: C-di-AMP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,96414
Polymers40,3801
Non-polymers1,58413
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.265, 110.265, 110.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: RNA chain C-di-AMP riboswitch


Mass: 40379.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcription
#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.: 11 / Source method: obtained synthetically / Formula: Mg

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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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: 0.5mM Spermine, 20mM Magnesium acetrate, 100mM Sodium achloride, 0.05M Sodium cacodylate pH6.5, 20%MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Dec 14, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. all: 9193 / Num. obs: 9173 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.05→3.11 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4QK8

4qk8


Resolution: 3.05→29.47 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 21.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 937 10.21 %RANDOM
Rwork0.1819 ---
obs0.1862 9173 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2516 99 0 2615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052916
X-RAY DIFFRACTIONf_angle_d0.9874547
X-RAY DIFFRACTIONf_dihedral_angle_d15.1931442
X-RAY DIFFRACTIONf_chiral_restr0.043601
X-RAY DIFFRACTIONf_plane_restr0.006121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.001-3.15910.28291320.23911169X-RAY DIFFRACTION100
3.1591-3.35670.26021280.20811159X-RAY DIFFRACTION100
3.3567-3.61550.22951340.20041155X-RAY DIFFRACTION100
3.6155-3.97860.22221300.17281186X-RAY DIFFRACTION100
3.9786-4.55240.22761360.16031157X-RAY DIFFRACTION100
4.5524-5.72870.1871340.16321191X-RAY DIFFRACTION100
5.7287-29.4710.22721430.18511219X-RAY DIFFRACTION99

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