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- PDB-6xus: RNA dodecamer with a 6-hydrazino-2-aminopurine modified base -

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Basic information

Entry
Database: PDB / ID: 6xus
TitleRNA dodecamer with a 6-hydrazino-2-aminopurine modified base
ComponentsRNA dodecamer with a 6-hydrazino-2-aminopurine modified base
KeywordsRNA / 6-hydrazino-2-aminopurine modified base
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsEnnifar, E. / Micura, R. / Gasser, C. / Brillet, K.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Thioguanosine Conversion Enables mRNA-Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC-seq DUAL).
Authors: Gasser, C. / Delazer, I. / Neuner, E. / Pascher, K. / Brillet, K. / Klotz, S. / Trixl, L. / Himmelstoss, M. / Ennifar, E. / Rieder, D. / Lusser, A. / Micura, R.
History
DepositionJan 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 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 dodecamer with a 6-hydrazino-2-aminopurine modified base
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9524
Polymers3,8811
Non-polymers703
Water1,892105
1
A: RNA dodecamer with a 6-hydrazino-2-aminopurine modified base
hetero molecules

A: RNA dodecamer with a 6-hydrazino-2-aminopurine modified base
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9038
Polymers7,7632
Non-polymers1416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1830 Å2
ΔGint-42 kcal/mol
Surface area4540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.120, 35.140, 31.870
Angle α, β, γ (deg.)90.000, 129.426, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1270-

HOH

21A-1290-

HOH

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Components

#1: RNA chain RNA dodecamer with a 6-hydrazino-2-aminopurine modified base


Mass: 3881.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: MPD, Na Cacodylate, spermine, NaCl, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 106381 / % possible obs: 99.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.68 Å2 / CC1/2: 1 / Rrim(I) all: 0.05 / Net I/σ(I): 13.32
Reflection shellResolution: 1.04→1.07 Å / Mean I/σ(I) obs: 0.29 / Num. unique obs: 1200 / CC1/2: 0.148 / Rrim(I) all: 261 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q1R

2q1r


Resolution: 1.1→24.62 Å / SU ML: 0.1782 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.5847
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1737 716 5 %
Rwork0.1531 13596 -
obs0.1542 14312 99.86 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.24 Å2
Refinement stepCycle: LAST / Resolution: 1.1→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 257 3 105 365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008306
X-RAY DIFFRACTIONf_angle_d1.8083476
X-RAY DIFFRACTIONf_chiral_restr0.03462
X-RAY DIFFRACTIONf_plane_restr0.033614
X-RAY DIFFRACTIONf_dihedral_angle_d6.4941142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.190.35781430.3272700X-RAY DIFFRACTION99.72
1.19-1.30.23781420.19682695X-RAY DIFFRACTION99.96
1.3-1.490.18781430.1592718X-RAY DIFFRACTION100
1.49-1.880.17521420.14552721X-RAY DIFFRACTION99.76
1.88-24.620.15351460.13852762X-RAY DIFFRACTION99.86

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