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- PDB-4fen: Crystal structure of the A24U/U25A/A46G mutant xpt-pbuX guanine r... -

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Basic information

Entry
Database: PDB / ID: 4fen
TitleCrystal structure of the A24U/U25A/A46G mutant xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine
ComponentsA24U/U25A/A46G mutant of the B. subtilis xpt-pbuX guanine riboswitch aptamer domain
KeywordsRNA / three-way junction with distal tertiary interaction / genetic regulatory element
Function / homologyACETATE ION / HYPOXANTHINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsStoddard, C.D. / Trausch, J.J. / Widmann, J. / Marcano, J. / Knight, R. / Batey, R.T.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Nucleotides Adjacent to the Ligand-Binding Pocket are Linked to Activity Tuning in the Purine Riboswitch.
Authors: Stoddard, C.D. / Widmann, J. / Trausch, J.J. / Marcano-Velazquez, J.G. / Knight, R. / Batey, R.T.
History
DepositionMay 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Feb 28, 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

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Assembly

Deposited unit
B: A24U/U25A/A46G mutant of the B. subtilis xpt-pbuX guanine riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,84610
Polymers21,5231
Non-polymers1,3239
Water10,773598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.689, 35.347, 41.388
Angle α, β, γ (deg.)90.00, 91.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-720-

HOH

21B-775-

HOH

31B-791-

HOH

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Components

#1: RNA chain A24U/U25A/A46G mutant of the B. subtilis xpt-pbuX guanine riboswitch aptamer domain


Mass: 21522.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 RNAP transcript
#2: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3K, 200 mM ammonium acetate, 10 mM cobalt hexammine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→40 Å / Num. all: 42755 / Num. obs: 40660 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.35→1.37 Å / % possible all: 66.7

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→40 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.191 3938 RANDOM
Rwork0.164 --
obs0.164 39278 -
all-42755 -
Refine analyzeLuzzati coordinate error obs: 0.13 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1423 63 598 2084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_bond_d0.009

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