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- PDB-3fu2: Cocrystal structure of a class-I preQ1 riboswitch -

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Basic information

Entry
Database: PDB / ID: 3fu2
TitleCocrystal structure of a class-I preQ1 riboswitch
ComponentsPreQ1 riboswitch
KeywordsRNA / aptamer / riboswitch / queuosine / PreQ1
Function / homology7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsKlein, D.J. / Edwards, T.E. / Ferre-D'Amare, A.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase
Authors: Klein, D.J. / Edwards, T.E. / Ferre-D'Amare, A.R.
History
DepositionJan 13, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Assembly

Deposited unit
A: PreQ1 riboswitch
B: PreQ1 riboswitch
C: PreQ1 riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,40515
Polymers32,5073
Non-polymers89812
Water37821
1
A: PreQ1 riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2157
Polymers10,8361
Non-polymers3806
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PreQ1 riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0954
Polymers10,8361
Non-polymers2593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PreQ1 riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0954
Polymers10,8361
Non-polymers2593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.208, 78.208, 85.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-906-

CA

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Components

#1: RNA chain PreQ1 riboswitch


Mass: 10835.524 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: Chemically synthesized RNA corresponding to the natural sequence from Bacillus subtilis
#2: Chemical ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H9N5O
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG 550 MME, 50 mM CaCl2, 100 mM Hepes-KOH pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 550 MME11
2CaCl211
3Hepes-KOH11
4PEG 550 MME12
5CaCl212
6Hepes-KOH1

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. all: 7147 / Num. obs: 7147 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Redundancy: 11.3 % / Rmerge(I) obs: 0.126
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.4 / % possible all: 68.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2669 390 Random
Rwork0.2144 --
all-7122 -
obs-7122 -
Refine analyze
ObsFree
Luzzati d res low5 Å-
Luzzati sigma a0.65 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 2.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1988 48 21 2057
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_bond_d0.053

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