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- PDB-6ibq: Structure of a nonameric RNA duplex at room temperature in ChipX ... -

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Basic information

Entry
Database: PDB / ID: 6ibq
TitleStructure of a nonameric RNA duplex at room temperature in ChipX microfluidic device
ComponentsDNA/RNA (5'-R(*CP*GP*UP*GP*AP*UP*CP*G)-D(P*C)-3')
KeywordsRNA / RNA duplex / GoU pair / chipx
Function / homologyDNA/RNA hybrid
Function and homology information
Biological speciesRattus (rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
Authorsde Wijn, R. / Olieric, V. / Lorber, B. / Sauter, C.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LABX-0057_MITOCROSS France
French National Research AgencyANR-10-LABX-0036_NETRNA France
France
Citation
Journal: Iucrj / Year: 2019
Title: A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography.
Authors: de Wijn, R. / Hennig, O. / Roche, J. / Engilberge, S. / Rollet, K. / Fernandez-Millan, P. / Brillet, K. / Betat, H. / Morl, M. / Roussel, A. / Girard, E. / Mueller-Dieckmann, C. / Fox, G.C. ...Authors: de Wijn, R. / Hennig, O. / Roche, J. / Engilberge, S. / Rollet, K. / Fernandez-Millan, P. / Brillet, K. / Betat, H. / Morl, M. / Roussel, A. / Girard, E. / Mueller-Dieckmann, C. / Fox, G.C. / Olieric, V. / Gavira, J.A. / Lorber, B. / Sauter, C.
#1: Journal: RNA / Year: 1999
Title: A sulfate pocket formed by three GoU pairs in the 0.97 A resolution X-ray structure of a nonameric RNA.
Authors: Masquida, B. / Sauter, C. / Westhof, E.
History
DepositionNov 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA/RNA (5'-R(*CP*GP*UP*GP*AP*UP*CP*G)-D(P*C)-3')
B: DNA/RNA (5'-R(*CP*GP*UP*GP*AP*UP*CP*G)-D(P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7603
Polymers5,6632
Non-polymers961
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-9 kcal/mol
Surface area3360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.000, 40.000, 69.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-101-

SO4

21A-102-

HOH

31A-107-

HOH

41B-211-

HOH

51B-220-

HOH

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*CP*GP*UP*GP*AP*UP*CP*G)-D(P*C)-3')


Mass: 2831.743 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rattus (rat)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 300 K / Method: counter-diffusion / pH: 6
Details: RNA solution: 10 mg/mL in 10 mM Na-cacodylate pH 6.0, 5 mM MgCl2. Reservoir solution: 2.6 M ammonium sulfate, 50 mM Na-cacodylate pH 6.0, 5 mM MgSO4, 1 mM spermine. Crystallization and ...Details: RNA solution: 10 mg/mL in 10 mM Na-cacodylate pH 6.0, 5 mM MgCl2. Reservoir solution: 2.6 M ammonium sulfate, 50 mM Na-cacodylate pH 6.0, 5 mM MgSO4, 1 mM spermine. Crystallization and crystallographic analysis were performed using the ChipX microfluidic device.

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: in situ / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 31, 2011
RadiationMonochromator: Bartel monochromator with dual channel cut crystals (DCCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→24 Å / Num. obs: 5485 / % possible obs: 91.5 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 23.6 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.157 / Rrim(I) all: 0.179 / Net I/σ(I): 6.1
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 304 / CC1/2: 0.755 / Rrim(I) all: 0.455 / % possible all: 69.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDS20180808data reduction
XSCALE20180808data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 485D

485d


Resolution: 1.55→23.037 Å / Cross valid method: THROUGHOUT / σ(F): 2.55 / Phase error: 25.79
Details: The structure was refined using data collected on four crystals at room temperature. The first nucleotide of each chain was not visible in the electron density and is not included in the model.
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 382 6.97 %Random selection
Rwork0.1924 ---
obs0.2073 5484 91.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→23.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 342 5 43 390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004384
X-RAY DIFFRACTIONf_angle_d0.68596
X-RAY DIFFRACTIONf_dihedral_angle_d8.74182
X-RAY DIFFRACTIONf_chiral_restr0.03178
X-RAY DIFFRACTIONf_plane_restr0.00316

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