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- PDB-7k16: Tamana Bat Virus xrRNA1 -

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Basic information

Entry
Database: PDB / ID: 7k16
TitleTamana Bat Virus xrRNA1
ComponentsRNA (51-MER)
KeywordsRNA / xrRNA / flavivirus / exoribonuclease-resitant / ncRNA / Tamana Bat Virus / XRN1
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesTamana bat virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJones, R.A. / Kieft, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118070 United States
CitationJournal: Rna / Year: 2021
Title: Different tertiary interactions create the same important 3D features in a distinct flavivirus xrRNA.
Authors: Jones, R.A. / Steckelberg, A.L. / Vicens, Q. / Szucs, M.J. / Akiyama, B.M. / Kieft, J.S.
History
DepositionSep 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
P: RNA (51-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5347
Polymers16,3901
Non-polymers1456
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Structure was experimentally shown to be Xrn1 resistant, supporting the folded stucture.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.100, 79.100, 40.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: RNA chain RNA (51-MER)


Mass: 16389.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tamana bat virus
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Mg2+chloride hexahydrate, 0.1M HEPES sodium (pH 7.5), and 30% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0972 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Feb 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0972 Å / Relative weight: 1
ReflectionResolution: 2.1→39.55 Å / Num. obs: 8806 / % possible obs: 99.9 % / Redundancy: 21.2 % / Biso Wilson estimate: 42.01 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.09495 / Rpim(I) all: 0.02102 / Rrim(I) all: 0.09728 / Net I/σ(I): 27.9
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 19.6 % / Rmerge(I) obs: 1.694 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 875 / CC1/2: 0.779 / CC star: 0.936 / Rpim(I) all: 0.3905 / Rrim(I) all: 1.739 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSVERSION Mar 15, 2019 BUILT=20191015data reduction
XDSVERSION Mar 15, 2019 BUILT=20191015data scaling
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OIU

2oiu


Resolution: 2.1→39.55 Å / SU ML: 0.2722 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4227
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2463 1423 8.57 %
Rwork0.1867 15184 -
obs0.1918 16607 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.71 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1088 6 54 1148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911215
X-RAY DIFFRACTIONf_angle_d1.23931893
X-RAY DIFFRACTIONf_chiral_restr0.0509254
X-RAY DIFFRACTIONf_plane_restr0.014551
X-RAY DIFFRACTIONf_dihedral_angle_d13.4142609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.28681420.26951539X-RAY DIFFRACTION99.88
2.18-2.260.36641430.28741504X-RAY DIFFRACTION99.7
2.26-2.370.30521480.26261493X-RAY DIFFRACTION99.33
2.37-2.490.30631420.24141508X-RAY DIFFRACTION99.7
2.49-2.650.37941440.24271533X-RAY DIFFRACTION99.82
2.65-2.850.27961400.23351528X-RAY DIFFRACTION99.76
2.85-3.140.23881380.18551499X-RAY DIFFRACTION99.88
3.14-3.590.22351380.15641513X-RAY DIFFRACTION100
3.59-4.520.20071460.15011541X-RAY DIFFRACTION100
4.52-39.550.22981420.16731526X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 46.3862311397 Å / Origin y: -11.5807944004 Å / Origin z: 21.3647912546 Å
111213212223313233
T0.374739413248 Å20.0204636695567 Å2-0.026892734432 Å2-0.294129864976 Å2-0.00666270246797 Å2--0.333194632205 Å2
L3.41119590679 °2-1.98326955535 °20.775992405133 °2-1.15381775044 °2-0.47659958355 °2--0.415240556063 °2
S-0.0649704357475 Å °0.0161906878516 Å °0.307355470804 Å °0.0303394429154 Å °0.00820123372835 Å °-0.165727022981 Å °-0.0904498802259 Å °0.00318787539878 Å °0.0583137039136 Å °
Refinement TLS groupSelection details: all

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