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- PDB-3la5: X-ray crystal structure of mc6 RNA Riboswitch bound to azacytosine -

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Basic information

Entry
Database: PDB / ID: 3la5
TitleX-ray crystal structure of mc6 RNA Riboswitch bound to azacytosine
ComponentsAdenosine RIboswitch
KeywordsRNA / Riboswitch / gene regulation / synthetic biology
Function / homology6-amino-1,3,5-triazin-2(1H)-one / RNA / RNA (> 10)
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDunstan, M.S. / Leys, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Reengineering orthogonally selective riboswitches
Authors: Dixon, N. / Duncan, J.N. / Geerlings, T. / Dunstan, M.S. / McCarthy, J.E.G. / Leys, D. / Micklefield, J.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_conn.ptnr2_label_seq_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: Adenosine RIboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,05612
Polymers22,7001
Non-polymers35511
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.845, 125.105, 24.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain Adenosine RIboswitch


Mass: 22700.432 Da / Num. of mol.: 1 / Mutation: U47C, U51C, U74C / Source method: obtained synthetically / Details: in vitro expression / Source: (synth.) Bacillus subtilis (bacteria)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-5AZ / 6-amino-1,3,5-triazin-2(1H)-one / 5-Azacytosine


Mass: 112.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4N4O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsU OF 47TH, 51TH AND 74TH WERE ENGINEERED TO C.

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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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 3M 1,6-hexanediol, 0.1M Tris-HCl (pH 9.0), 200mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→26.083 Å / Num. all: 24047 / Num. obs: 23579 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 15.63 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 16.88
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 5.25 / Num. unique all: 3073 / Rsym value: 0.308 / % possible all: 80.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y26

1y26


Resolution: 1.7→26.08 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.87 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1247 5.3 %Random
Rwork0.18 ---
obs0.181 23538 98.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.361 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 83.59 Å2 / Biso mean: 24.817 Å2 / Biso min: 8.03 Å2
Baniso -1Baniso -2Baniso -3
1-2.135 Å2-0 Å20 Å2
2---2.907 Å2-0 Å2
3---0.771 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1503 18 382 1903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051686
X-RAY DIFFRACTIONf_angle_d1.2292620
X-RAY DIFFRACTIONf_chiral_restr0.059355
X-RAY DIFFRACTIONf_plane_restr0.00672
X-RAY DIFFRACTIONf_dihedral_angle_d19.805707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.7680.2141090.1972082219184
1.768-1.8490.2431310.19124572588100
1.849-1.9460.2351530.19624762629100
1.946-2.0680.2581520.18924642616100
2.068-2.2280.241430.19225062649100
2.228-2.4520.2571320.19625142646100
2.452-2.8060.2071360.20125412677100
2.806-3.5340.1651490.15625612710100
3.534-26.0830.1571420.162690283299

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