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- PDB-8ami: Crystal structure of AUGUGGCAU duplex with barium ions (model 2) -

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Basic information

Entry
Database: PDB / ID: 8ami
TitleCrystal structure of AUGUGGCAU duplex with barium ions (model 2)
ComponentsRNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
KeywordsRNA / UG wobble / Ba ions / UGG repeats
Function / homology: / RNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsKiliszek, A. / Rypniewski, W.
Funding support Poland, 1items
OrganizationGrant numberCountry
Other government Poland
CitationJournal: Rna / Year: 2022
Title: Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.
Authors: Kiliszek, A. / Pluta, M. / Bejger, M. / Rypniewski, W.
History
DepositionAug 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
B: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0435
Polymers5,7462
Non-polymers2983
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-34 kcal/mol
Surface area3160 Å2
Unit cell
Length a, b, c (Å)34.109, 34.109, 81.353
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-220-

HOH

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Components

#1: RNA chain RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Mass: 2872.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.08 M NaCl 0.02 M BaCl2 0.04 M cacodylate sodium 45% MPD 0.012 M spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 1.79→31.5 Å / Num. obs: 8634 / % possible obs: 99.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 21.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.49
Reflection shellResolution: 1.79→1.9 Å / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 1386 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AMG

8amg


Resolution: 1.79→31.46 Å / SU ML: 0.2192 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1995
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2361 428 4.96 %
Rwork0.1825 8201 -
obs0.185 8629 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.47 Å2
Refinement stepCycle: LAST / Resolution: 1.79→31.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 380 3 42 425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005451
X-RAY DIFFRACTIONf_angle_d0.9307703
X-RAY DIFFRACTIONf_chiral_restr0.036793
X-RAY DIFFRACTIONf_plane_restr0.006519
X-RAY DIFFRACTIONf_dihedral_angle_d10.3616223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-2.050.30931420.23892726X-RAY DIFFRACTION99.31
2.05-2.580.28171390.1992738X-RAY DIFFRACTION99.93
2.58-31.460.19921470.1612737X-RAY DIFFRACTION99.65

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