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- PDB-4fe5: Crystal structure of the xpt-pbuX guanine riboswitch aptamer doma... -

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Basic information

Entry
Database: PDB / ID: 4fe5
TitleCrystal structure of the xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine
Componentsxpt-pbuX guanine riboswitch aptamer domain
KeywordsRNA / three-way junction with distal tertiary interaction / gene regulatory element / hypoxanthine
Function / homologyACETATE ION / HYPOXANTHINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsStoddard, C.D. / Trausch, J.J. / Widmann, J. / Marcano, J. / Knight, R. / Batey, R.T.
CitationJournal: Nature / Year: 2004
Title: Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine.
Authors: Batey, R.T. / Gilbert, S.D. / Montange, R.K.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionJun 27, 2012ID: 1U8D
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 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: xpt-pbuX guanine riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,72810
Polymers21,5071
Non-polymers1,2219
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.247, 35.250, 41.833
Angle α, β, γ (deg.)90.00, 90.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain xpt-pbuX guanine riboswitch aptamer domain


Mass: 21506.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 RNA 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.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 46.14 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2005
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.32→20 Å / Num. all: 45993 / Num. obs: 42571 / % possible obs: 92.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.8
Reflection shellResolution: 1.32→1.37 Å / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.3 / % possible all: 54.5

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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: 1.32→20 Å / σ(F): 2.3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.229 2129 RANDOM
Rwork0.196 --
obs0.196 42404 -
all-45993 -
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-1.32 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.32→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1422 60 538 2020
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.385
X-RAY DIFFRACTIONc_dihedral_angle_d20.53
X-RAY DIFFRACTIONc_improper_angle_d1.603

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