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- PDB-8amj: Crystal structure of unliganded AUGUGGCAU duplex -

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Basic information

Entry
Database: PDB / ID: 8amj
TitleCrystal structure of unliganded AUGUGGCAU duplex
ComponentsRNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
KeywordsRNA / UG wobble / Ba ions / UGG repeats
Function / homologyACETATE ION / RNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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)6,1897
Polymers5,7462
Non-polymers4435
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-37 kcal/mol
Surface area3740 Å2
Unit cell
Length a, b, c (Å)49.124, 49.124, 69.729
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11B-101-

SO4

21B-101-

SO4

31B-103-

SO4

41B-103-

SO4

51B-208-

HOH

61B-210-

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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 10mM AcOMg 50mM MES pH5.6 2.5M AS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.89429 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89429 Å / Relative weight: 1
ReflectionResolution: 2.02→26.97 Å / Num. obs: 4105 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 40.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.78
Reflection shellResolution: 2.02→2.14 Å / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 653 / CC1/2: 0.737

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Processing

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

8ami


Resolution: 2.02→26.97 Å / SU ML: 0.1931 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 31.5739
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2428 410 10.01 %
Rwork0.1968 3686 -
obs0.2015 4096 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.32 Å2
Refinement stepCycle: LAST / Resolution: 2.02→26.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 380 24 21 425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066443
X-RAY DIFFRACTIONf_angle_d0.9197685
X-RAY DIFFRACTIONf_chiral_restr0.039388
X-RAY DIFFRACTIONf_plane_restr0.004919
X-RAY DIFFRACTIONf_dihedral_angle_d7.5232208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.310.28261370.23941228X-RAY DIFFRACTION99.93
2.31-2.910.32911370.27391232X-RAY DIFFRACTION100
2.91-26.970.20791360.1641226X-RAY DIFFRACTION98.98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.014899356920.14764187216-0.2506822647471.682796854570.2705922269962.021586678520.4015355927610.04102914184840.273453716919-0.09437032705320.159552814567-0.44927746365-0.09108034083620.208792868291-0.5362350495870.3851161317370.01736321781360.07847733396930.353576785703-0.1475234119390.37432296632-13.8803177187-13.63241307097.02605154
23.84968946821-0.213726874648-2.174281295431.595282849260.6056026865553.334357889550.446401054313-0.08514281557470.500460783648-0.280661410610.187617056355-0.625362764088-0.3364219711940.596141267444-0.6103212454610.336800018212-0.0377383347920.08669911290420.401130575307-0.1561406270420.429387159673-12.7311970135-10.755095531511.2538715517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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