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- PDB-5tpy: Crystal structure of an exonuclease resistant RNA from Zika virus -

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Basic information

Entry
Database: PDB / ID: 5tpy
TitleCrystal structure of an exonuclease resistant RNA from Zika virus
ComponentsRNA (71-MER)
KeywordsRNA / Zika RNA exonuclease resistance
Function / homologyHEXANE-1,6-DIOL / RNA / RNA (> 10)
Function and homology information
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.805 Å
AuthorsAkiyama, B.M. / Laurence, H.M. / Massey, A.R. / Costantino, D.A. / Xie, X. / Yang, Y. / Shi, P.-Y. / Nix, J.C. / Beckham, J.D. / Kieft, J.S.
CitationJournal: Science / Year: 2016
Title: Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease.
Authors: Akiyama, B.M. / Laurence, H.M. / Massey, A.R. / Costantino, D.A. / Xie, X. / Yang, Y. / Shi, P.Y. / Nix, J.C. / Beckham, J.D. / Kieft, J.S.
History
DepositionOct 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1603
Polymers23,0181
Non-polymers1422
Water18010
1
A: RNA (71-MER)
hetero molecules

A: RNA (71-MER)
hetero molecules

A: RNA (71-MER)
hetero molecules

A: RNA (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,64112
Polymers92,0714
Non-polymers5708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area6770 Å2
ΔGint-71 kcal/mol
Surface area41680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.679, 111.679, 90.826
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: RNA chain RNA (71-MER)


Mass: 23017.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MR766-NIID / Source: (synth.) Zika virus
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: drop: 1 uL 5 mg/mL RNA in 2.5 mM magnesium chloride, 10 mM HEPES-KOH pH 7.5 (heated to 65 C for 3 minutes, cooled at room temperature, 0.5 mM spermidine added, centrifuged for 10 minutes at ...Details: drop: 1 uL 5 mg/mL RNA in 2.5 mM magnesium chloride, 10 mM HEPES-KOH pH 7.5 (heated to 65 C for 3 minutes, cooled at room temperature, 0.5 mM spermidine added, centrifuged for 10 minutes at 13000 x g) + 1 uL 50 mM sodium cacodylate pH 6.0, 150 mM NaCl, 4 mM CaCl2, 0.6 mM spermine, 36% 1,6-hexanediol. Crystals were flash-frozen in the mother liquor using liquid nitrogen for x-ray diffraction.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0972 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0972 Å / Relative weight: 1
ReflectionResolution: 2.805→55.839 Å / Num. obs: 15501 / % possible obs: 99.6 % / Redundancy: 21.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 31.5
Reflection shellResolution: 2.81→2.91 Å / Redundancy: 21.1 % / Rmerge(I) obs: 1.492 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.82 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2499: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pqv

4pqv


Resolution: 2.805→55.839 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5
RfactorNum. reflection% reflection
Rfree0.2177 1532 9.88 %
Rwork0.1906 --
obs0.1933 15501 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.805→55.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1527 9 10 1546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061716
X-RAY DIFFRACTIONf_angle_d1.1032671
X-RAY DIFFRACTIONf_dihedral_angle_d12.49854
X-RAY DIFFRACTIONf_chiral_restr0.045355
X-RAY DIFFRACTIONf_plane_restr0.00771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8046-2.89510.38661360.33051257X-RAY DIFFRACTION99
2.8951-2.99860.32521340.30221280X-RAY DIFFRACTION100
2.9986-3.11860.35621420.27671280X-RAY DIFFRACTION100
3.1186-3.26050.2341400.21611255X-RAY DIFFRACTION100
3.2605-3.43240.21911490.20231287X-RAY DIFFRACTION100
3.4324-3.64740.24691360.18951261X-RAY DIFFRACTION100
3.6474-3.9290.19921450.17121267X-RAY DIFFRACTION100
3.929-4.32420.15721380.15541280X-RAY DIFFRACTION100
4.3242-4.94960.18081410.1421273X-RAY DIFFRACTION100
4.9496-6.23470.18091360.15681279X-RAY DIFFRACTION100
6.2347-55.85050.22981350.21331250X-RAY DIFFRACTION97

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