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- PDB-8amg: Crystal structure of AUGUGGCAU duplex with barium ions (model 1) -

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Basic information

Entry
Database: PDB / ID: 8amg
TitleCrystal structure of AUGUGGCAU duplex with barium ions (model 1)
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 / SAD / Resolution: 2.26 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 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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')
C: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
D: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
E: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
F: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
G: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
H: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
I: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
J: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
K: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
L: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,12124
Polymers34,47312
Non-polymers1,64812
Water1,18966
1
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)6,0204
Polymers5,7462
Non-polymers2752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-36 kcal/mol
Surface area3080 Å2
2
C: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
D: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0204
Polymers5,7462
Non-polymers2752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-35 kcal/mol
Surface area3120 Å2
3
E: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
F: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0204
Polymers5,7462
Non-polymers2752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-35 kcal/mol
Surface area3130 Å2
4
G: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
H: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0204
Polymers5,7462
Non-polymers2752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-36 kcal/mol
Surface area3120 Å2
5
I: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
J: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0204
Polymers5,7462
Non-polymers2752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-36 kcal/mol
Surface area3120 Å2
6
K: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
L: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0204
Polymers5,7462
Non-polymers2752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-35 kcal/mol
Surface area3140 Å2
Unit cell
Length a, b, c (Å)84.014, 84.014, 138.966
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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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.: 12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.05 Å3/Da / Density % sol: 40.1 %
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 26, 2016 / Details: M
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 2.26→42.01 Å / Num. obs: 25605 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 45.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.73
Reflection shellResolution: 2.26→2.4 Å / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 4153 / CC1/2: 0.619 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.26→42.01 Å / SU ML: 0.2627 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2361
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2404 1274 4.98 %
Rwork0.1909 24317 -
obs0.1934 25591 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.65 Å2
Refinement stepCycle: LAST / Resolution: 2.26→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2280 12 66 2358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572598
X-RAY DIFFRACTIONf_angle_d1.06214038
X-RAY DIFFRACTIONf_chiral_restr0.0414538
X-RAY DIFFRACTIONf_plane_restr0.006110
X-RAY DIFFRACTIONf_dihedral_angle_d10.5591278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.350.32211410.29462697X-RAY DIFFRACTION99.82
2.35-2.460.3691460.28282709X-RAY DIFFRACTION99.93
2.46-2.590.33041430.28432688X-RAY DIFFRACTION100
2.59-2.750.35461350.2762726X-RAY DIFFRACTION99.97
2.75-2.960.26471450.25692698X-RAY DIFFRACTION99.93
2.96-3.260.25521470.21082710X-RAY DIFFRACTION99.93
3.26-3.730.24921330.21492708X-RAY DIFFRACTION100
3.73-4.70.25751400.14252708X-RAY DIFFRACTION100
4.7-42.010.12761440.11522673X-RAY DIFFRACTION98.36

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