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- PDB-4qka: c-di-AMP riboswitch from Thermoanaerobacter pseudethanolicus, iri... -

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Basic information

Entry
Database: PDB / ID: 4qka
Titlec-di-AMP riboswitch from Thermoanaerobacter pseudethanolicus, iridium hexamine soak
ComponentsC-di-AMP riboswitch
KeywordsRNA / c-di-AMP riboswitch
Function / homologyChem-2BA / IRIDIUM HEXAMMINE ION / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 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 1.3Feb 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_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_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_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: C-di-AMP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,67111
Polymers39,7221
Non-polymers2,94810
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.035, 116.035, 114.098
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain C-di-AMP riboswitch


Mass: 39722.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcription

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Non-polymers , 6 types, 12 molecules

#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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H18IrN6
#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: 5.58 Å3/Da / Density % sol: 77.97 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.3
Details: 1.5 M (NH4)2SO4, 0.1M HEPES, pH 7.3, and 0.2 M Li2SO4, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.105 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 28391 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.2→3.31 Å / % possible all: 99.7

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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: SAD / Resolution: 3.2→29.009 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2863 10.08 %RANDOM
Rwork0.1714 ---
obs0.1739 28391 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→29.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2578 130 2 2710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053019
X-RAY DIFFRACTIONf_angle_d1.0494737
X-RAY DIFFRACTIONf_dihedral_angle_d18.5061478
X-RAY DIFFRACTIONf_chiral_restr0.047614
X-RAY DIFFRACTIONf_plane_restr0.005124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.194-3.2490.38381410.31961254X-RAY DIFFRACTION98
3.249-3.3080.33821370.27511280X-RAY DIFFRACTION98
3.308-3.37160.31541460.27041230X-RAY DIFFRACTION99
3.3716-3.44030.26991340.26131300X-RAY DIFFRACTION99
3.4403-3.5150.32911410.251292X-RAY DIFFRACTION100
3.515-3.59660.30591400.26131267X-RAY DIFFRACTION100
3.5966-3.68640.231440.23841268X-RAY DIFFRACTION100
3.6864-3.78580.30841480.22591293X-RAY DIFFRACTION100
3.7858-3.8970.22191440.20291262X-RAY DIFFRACTION100
3.897-4.02240.21871380.19151285X-RAY DIFFRACTION100
4.0224-4.16580.18741480.1921278X-RAY DIFFRACTION100
4.1658-4.33210.21151340.17651285X-RAY DIFFRACTION100
4.3321-4.52850.18031440.16481287X-RAY DIFFRACTION100
4.5285-4.76630.15271480.1631274X-RAY DIFFRACTION100
4.7663-5.06350.17061500.15381276X-RAY DIFFRACTION100
5.0635-5.4520.15841440.13511285X-RAY DIFFRACTION100
5.452-5.99630.15991400.14291272X-RAY DIFFRACTION100
5.9963-6.8540.14421500.13091285X-RAY DIFFRACTION100
6.854-8.59790.16391500.13251268X-RAY DIFFRACTION100
8.5979-29.00990.17591420.12591287X-RAY DIFFRACTION100

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