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- PDB-5c7w: 5'-monophosphate Z:P Guanine Riboswitch bound to hypoxanthine. -

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Basic information

Entry
Database: PDB / ID: 5c7w
Title5'-monophosphate Z:P Guanine Riboswitch bound to hypoxanthine.
Components5'-monophosphate Z:P guanine riboswitch
KeywordsRNA / expanded RNA / riboswitch / Unnatural base pair
Function / homologyHYPOXANTHINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsHernandez, A.R. / Shao, Y. / Hoshika, S. / Yang, Z. / Shelke, S.A. / Herrou, J. / Kim, H.-J. / Kim, M.-J. / Piccirilli, J.A. / Benner, S.A.
Funding support United States, 3items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)HDTRA1-13-1-0004 United States
National Aeronautic Space Administration (NASA, United States)NNX10AT28G United States
Templeton World Charitable Fund United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair.
Authors: Hernandez, A.R. / Shao, Y. / Hoshika, S. / Yang, Z. / Shelke, S.A. / Herrou, J. / Kim, H.J. / Kim, M.J. / Piccirilli, J.A. / Benner, S.A.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0May 1, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-monophosphate Z:P guanine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,97610
Polymers21,5511
Non-polymers1,4259
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)52.180, 52.180, 274.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: RNA chain 5'-monophosphate Z:P guanine riboswitch


Mass: 21550.793 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 1000, 240 mM NH4OAc, 10 mM K-HEPES, 10 mM Co(NH3)6Cl3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.22→44.59 Å / Num. obs: 4107 / % possible obs: 99.8 % / Redundancy: 8.54 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 24.9
Reflection shellResolution: 3.22→3.34 Å / Redundancy: 8.95 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SCALAdata scaling
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FE5

4fe5


Resolution: 3.22→42.923 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2797 220 5.36 %Random selection
Rwork0.2277 ---
obs0.2308 3887 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.22→42.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1428 66 0 1494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011654
X-RAY DIFFRACTIONf_angle_d1.8022618
X-RAY DIFFRACTIONf_dihedral_angle_d17.134837
X-RAY DIFFRACTIONf_chiral_restr0.068334
X-RAY DIFFRACTIONf_plane_restr0.0169
LS refinement shellResolution: 3.2204→4.0569 Å
RfactorNum. reflection% reflection
Rfree0.3071 109 -
Rwork0.2335 1861 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -7.5373 Å / Origin y: -11.246 Å / Origin z: 4.2317 Å
111213212223313233
T0.9364 Å2-0.1644 Å2-0.115 Å2-0.4938 Å2-0.0494 Å2--0.825 Å2
L1.4356 °2-1.6881 °20.5383 °2-3.1439 °2-0.1706 °2--1.2401 °2
S0.2268 Å °0.0051 Å °0.051 Å °0.0529 Å °-0.0878 Å °-1.0337 Å °0.2506 Å °-0.0281 Å °0.3173 Å °
Refinement TLS groupSelection details: all

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