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- PDB-4phy: Functional conservation despite structural divergence in ligand-r... -

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Basic information

Entry
Database: PDB / ID: 4phy
TitleFunctional conservation despite structural divergence in ligand-responsive RNA switches
Components
  • RNA (26-MER)
  • RNA (5'-R(*GP*CP*AP*GP*GP*AP*AP*CP*CP*GP*AP*GP*AP*GP*GP*CP*AP*CP*GP*C)-3')
KeywordsRNA / Viral genome / internal ribosome entry site / translation
Function / homologyACETATE ION / RNA / RNA (> 10)
Function and homology information
Biological speciesSeneca valley virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBoerneke, M.A. / Dibrov, S.M. / Hermann, T.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Functional conservation despite structural divergence in ligand-responsive RNA switches.
Authors: Boerneke, M.A. / Dibrov, S.M. / Gu, J. / Wyles, D.L. / Hermann, T.
History
DepositionMay 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (26-MER)
B: RNA (5'-R(*GP*CP*AP*GP*GP*AP*AP*CP*CP*GP*AP*GP*AP*GP*GP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8976
Polymers14,7302
Non-polymers1674
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-13 kcal/mol
Surface area8910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.611, 79.611, 100.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: RNA chain RNA (26-MER)


Mass: 8206.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Seneca valley virus
#2: RNA chain RNA (5'-R(*GP*CP*AP*GP*GP*AP*AP*CP*CP*GP*AP*GP*AP*GP*GP*CP*AP*CP*GP*C)-3')


Mass: 6523.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Seneca valley virus
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: KCl, Magnesium Acetate, PEG 8K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→19.9 Å / Num. all: 3319 / Num. obs: 3167 / % possible obs: 88.15 % / Redundancy: 28 % / Net I/σ(I): 22.28
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 15.5 % / Mean I/σ(I) obs: 2.5 / % possible all: 56.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→19.375 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 152 4.58 %Random selection
Rwork0.2148 ---
obs0.2173 3167 88.15 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.991 Å2 / ksol: 0.243 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.0187 Å2-0 Å20 Å2
2---14.0187 Å2-0 Å2
3---31.5952 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 974 10 0 984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071093
X-RAY DIFFRACTIONf_angle_d1.071697
X-RAY DIFFRACTIONf_dihedral_angle_d17.489544
X-RAY DIFFRACTIONf_chiral_restr0.057228
X-RAY DIFFRACTIONf_plane_restr0.00548
LS refinement shellResolution: 3.1→19.3749 Å
RfactorNum. reflection% reflection
Rfree0.2679 152 -
Rwork0.2148 3167 -
obs--88 %
Refinement TLS params.Method: refined / Origin x: 15.5746 Å / Origin y: -25.3019 Å / Origin z: -13.2805 Å
111213212223313233
T0.6227 Å2-0.0541 Å20.0644 Å2-0.5997 Å20.0467 Å2--0.6559 Å2
L2.1701 °20.1177 °2-1.0871 °2-2.6812 °2-0.4093 °2--1.6609 °2
S0.1863 Å °-0.2615 Å °-0.2015 Å °0.8412 Å °-0.0802 Å °1.1959 Å °-0.2822 Å °0.2079 Å °0.095 Å °
Refinement TLS groupSelection details: all

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