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- PDB-4qlm: ydao riboswitch binding to c-di-AMP -

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Basic information

Entry
Database: PDB / ID: 4qlm
Titleydao riboswitch binding to c-di-AMP
ComponentsRNA (108-MER)
KeywordsRNA / second message molecule / c-di-AMP binding
Function / homologyChem-2BA / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.721 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 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
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_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

Downloads & links

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Assembly

Deposited unit
A: RNA (108-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0727
Polymers40,5141
Non-polymers1,5586
Water59433
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.767, 87.975, 145.235
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 (108-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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.11 Å3/Da / Density % sol: 60.39 %
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 / Wavelength: 0.9792
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.721→50 Å / Num. obs: 13840 / % possible obs: 99.7 % / Observed criterion σ(I): 1.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL2Mapmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.721→45.64 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 32.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 690 4.87 %
Rwork0.213 --
obs0.215 12971 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.721→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2316 100 33 2449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012730
X-RAY DIFFRACTIONf_angle_d1.6984254
X-RAY DIFFRACTIONf_dihedral_angle_d21.2191324
X-RAY DIFFRACTIONf_chiral_restr0.057560
X-RAY DIFFRACTIONf_plane_restr0.007113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6919-2.89970.41441360.39042566X-RAY DIFFRACTION96
2.8997-3.19140.33481420.29512668X-RAY DIFFRACTION100
3.1914-3.6530.26481280.21922723X-RAY DIFFRACTION100
3.653-4.60180.23891360.19392727X-RAY DIFFRACTION100
4.6018-45.64910.20671480.19042795X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.8744 Å / Origin y: 30.0921 Å / Origin z: -16.4253 Å
111213212223313233
T0.5715 Å20.0629 Å2-0.1144 Å2-0.8722 Å2-0.3618 Å2--0.7221 Å2
L3.258 °2-0.3108 °21.1355 °2-0.993 °2-0.4407 °2--2.4297 °2
S-0.121 Å °-0.9047 Å °0.7806 Å °0.0647 Å °-0.226 Å °0.083 Å °-0.1386 Å °-0.1881 Å °0.2949 Å °
Refinement TLS groupSelection details: all

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