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- PDB-6ymc: 26-mer stem-loop RNA -

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Basic information

Entry
Database: PDB / ID: 6ymc
Title26-mer stem-loop RNA
ComponentsRNA (26-MER)
KeywordsRNA / tetra-loop
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJanowski, R. / Niessing, D.
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation.
Authors: Niedner-Boblenz, A. / Monecke, T. / Hennig, J. / Klostermann, M. / Hofweber, M. / Davydova, E. / Gerber, A.P. / Anosova, I. / Mayer, W. / Muller, M. / Heym, R.G. / Janowski, R. / Paillart, J. ...Authors: Niedner-Boblenz, A. / Monecke, T. / Hennig, J. / Klostermann, M. / Hofweber, M. / Davydova, E. / Gerber, A.P. / Anosova, I. / Mayer, W. / Muller, M. / Heym, R.G. / Janowski, R. / Paillart, J.C. / Dormann, D. / Zarnack, K. / Sattler, M. / Niessing, D.
History
DepositionApr 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Mar 12, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (26-MER)
B: RNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,11112
Polymers16,7382
Non-polymers1,37310
Water1,74797
1
A: RNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0566
Polymers8,3691
Non-polymers6875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0566
Polymers8,3691
Non-polymers6875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.270, 52.430, 107.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (26-MER)


Mass: 8369.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM NaCl, 15 mM BaCl2, 40 mM Na Cacodylate 7.0 44 % MPD, 12 mM spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50.01 Å / Num. obs: 9048 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 31.5 Å2 / CC1/2: 0.987 / Net I/σ(I): 13.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.49 / Num. unique obs: 750 / CC1/2: 0.681 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.846 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.181
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 488 5.1 %RANDOM
Rwork0.1752 ---
obs0.1784 9048 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.77 Å2 / Biso mean: 31.496 Å2 / Biso min: 15.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0 Å2-0 Å2
2--1.54 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1108 10 97 1215
Biso mean--40.82 33.81 -
Num. residues----52
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0111240
X-RAY DIFFRACTIONr_bond_other_d0.0050.02508
X-RAY DIFFRACTIONr_angle_refined_deg2.2781.2761930
X-RAY DIFFRACTIONr_angle_other_deg1.9331236
X-RAY DIFFRACTIONr_chiral_restr0.1110.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0270.02618
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02270
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 22 -
Rwork0.256 648 -
all-670 -
obs--95.44 %
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)
10.2535-0.11460.02180.15570.09740.1289-0.0309-0.0837-0.0808-0.08820.04220.0128-0.1282-0.0256-0.01130.13360.02650.00550.077-0.00250.058111.890330.1271.9292
20.96760.2610.19840.38910.50610.69140.0915-0.042-0.1327-0.1464-0.0328-0.0673-0.2252-0.0717-0.05870.09910.01610.00270.0869-0.01850.030220.489737.003534.4727
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 26
2X-RAY DIFFRACTION2B1 - 26

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