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- PDB-4fep: Crystal structure of the A24U/U25A/A46G/C74U mutant xpt-pbuX guan... -

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Basic information

Entry
Database: PDB / ID: 4fep
TitleCrystal structure of the A24U/U25A/A46G/C74U mutant xpt-pbuX guanine riboswitch aptamer domain in complex with 2,6-diaminopurine
ComponentsA24U/U25A/A46G/C74U mutant of the B. subtilis xpt-pbuX guanine riboswitch aptamer domain
KeywordsRNA / three-way junction with distal tertiary interaction / genetic regulatory element / 2 / 6-diaminopurine
Function / homology9H-PURINE-2,6-DIAMINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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:
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Assembly

Deposited unit
B: A24U/U25A/A46G/C74U mutant of the B. subtilis xpt-pbuX guanine riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,12411
Polymers21,5241
Non-polymers1,60010
Water10,287571
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.071, 35.252, 41.855
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain A24U/U25A/A46G/C74U mutant of the B. subtilis xpt-pbuX guanine riboswitch aptamer domain


Mass: 21523.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 RNAP transcript
#2: Chemical ChemComp-6AP / 9H-PURINE-2,6-DIAMINE / 2,6-DIAMINOPURINE


Mass: 150.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N6
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.28 Å3/Da / Density % sol: 46.05 %

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Data collection

DiffractionMean temperature: 100 K
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: 1.65→40 Å / Num. all: 23255 / Num. obs: 22255 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.65→1.68 Å / % possible all: 65.8

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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: 1.65→40 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.229 2059 RANDOM
Rwork0.179 --
obs0.179 20703 -
all-23255 -
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1423 74 571 2068
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.724
X-RAY DIFFRACTIONc_bond_d0.003

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