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- PDB-3gca: The structural basis for recognition of the preQ0 metabolite by a... -

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Basic information

Entry
Database: PDB / ID: 3gca
TitleThe structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain
ComponentsPreQ1 riboswitch
KeywordsRNA / PreQ1 / PreQ0 / riboswitch / ribosomal binding site / amptamer / metabolite
Function / homologyChem-PQ0 / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
AuthorsSpitale, R.C. / Wedekind, J.E.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain.
Authors: Spitale, R.C. / Torelli, A.T. / Krucinska, J. / Bandarian, V. / Wedekind, J.E.
History
DepositionFeb 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PreQ1 riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9674
Polymers10,5991
Non-polymers3673
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.5, 110.5, 59.31
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: RNA chain PreQ1 riboswitch


Mass: 10599.417 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The RNA strand was chemically synthesized based on the sequence of Class I, Type I PreQ1 riboswitch aptamer domain from T. tengcongensis
#2: Chemical ChemComp-PQ0 / 2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE / 7-DEAZA-7-CYANO-GUANINE


Mass: 175.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5N5O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 4.93 Å3/Da / Density % sol: 75.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.8 M Li2SO4, 0.10 M Na-cacodylate pH 6.0, 0.01 M Mg(SO4)2-, 5% (v/v) 1,3-propanediol and 2 mM spermine., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Li2SO411
2Na-cacodylate11
3Mg(SO4)211
41,3-Propanediol11
5Spermine11
6Li2SO412
7Na-cacodylate12
8Mg(SO4)212
91,3-Propanediol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1395, 1.1407, 0.97622, 1.1395
DetectorType: Quantum 315 CCD detector / Detector: CCD / Date: Jan 29, 2009
Details: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.13951
21.14071
30.976221
ReflectionResolution: 2.75→50 Å / Num. obs: 5990 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16.6 % / Biso Wilson estimate: 75 Å2 / Rsym value: 0.056 / Net I/σ(I): 36.47
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 15.8 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 579 / Rsym value: 0.36 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.75→28.33 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 303382.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS 1.2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.272 441 8 %RANDOM
Rwork0.245 ---
obs-5990 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.0924 Å2 / ksol: 0.2 e/Å3
Displacement parametersBiso mean: 76 Å2
Baniso -1Baniso -2Baniso -3
1--21 Å2--
2---21 Å2-
3---42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.75→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 702 23 0 725
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d1.99
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.487 65 8.2 %
Rwork0.438 728 -
obs--83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rnaATTdna-rnaATT
X-RAY DIFFRACTION2pqpq
X-RAY DIFFRACTION4to
X-RAY DIFFRACTION3ion.top

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