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- PDB-5mrx: 27-nt SRL with a 5-hydroxymethyl cytidine modification -

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Basic information

Entry
Database: PDB / ID: 5mrx
Title27-nt SRL with a 5-hydroxymethyl cytidine modification
ComponentsRNA (27-MER)
KeywordsRNA / modification / tetraloop
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.851 Å
AuthorsEnnifar, E. / Micura, R.
CitationJournal: J.Org.Chem. / Year: 2017
Title: Synthesis, Thermodynamic Properties, and Crystal Structure of RNA Oligonucleotides Containing 5-Hydroxymethylcytosine
Authors: Riml, C. / Lusser, A. / Ennifar, E. / Micura, R.
History
DepositionDec 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Mar 30, 2022Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: RNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)8,7741
Polymers8,7741
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.510, 29.510, 76.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: RNA chain RNA (27-MER)


Mass: 8774.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MRC=5hydroxymethyl-cytosine / Source: (synth.) Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.91 Å3/Da / Density % sol: 35.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: well: 3.0M (NH4)2SO4 drop: 50mM KMops pH7.0, 10mM MnCl2, 10mM MgCl2, 1.0mM Na-EDTA pH 8.0, 10mM Tris pH 8.0, RNA 2.5mg/ml 2vol drop + 1vol well

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.77 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77 Å / Relative weight: 1
ReflectionResolution: 0.85→50 Å / Num. obs: 57106 / % possible obs: 99.6 % / Redundancy: 22.36 % / Rrim(I) all: 0.045 / Net I/σ(I): 30.32

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dvz

3dvz


Resolution: 0.851→29.51 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.78
RfactorNum. reflection% reflection
Rfree0.1682 2870 5.03 %
Rwork0.1453 --
obs0.1587 57106 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.851→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 581 0 211 792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006707
X-RAY DIFFRACTIONf_angle_d1.1231107
X-RAY DIFFRACTIONf_dihedral_angle_d12.481347
X-RAY DIFFRACTIONf_chiral_restr0.047147
X-RAY DIFFRACTIONf_plane_restr0.01330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8509-0.86550.44681360.41122577X-RAY DIFFRACTION89
0.8655-0.88130.40581390.36462649X-RAY DIFFRACTION93
0.8813-0.89820.35151430.33922711X-RAY DIFFRACTION95
0.8982-0.91660.3181430.3182720X-RAY DIFFRACTION95
0.9166-0.93650.29621420.28242694X-RAY DIFFRACTION95
0.9365-0.95830.26131450.26492751X-RAY DIFFRACTION95
0.9583-0.98220.2391430.22822721X-RAY DIFFRACTION95
0.9822-1.00880.20141420.20742687X-RAY DIFFRACTION95
1.0088-1.03850.19191430.18942732X-RAY DIFFRACTION95
1.0385-1.0720.18451420.17762699X-RAY DIFFRACTION95
1.072-1.11030.18781440.18032725X-RAY DIFFRACTION95
1.1103-1.15480.16931430.1772721X-RAY DIFFRACTION95
1.1548-1.20730.19581430.17672722X-RAY DIFFRACTION95
1.2073-1.2710.16281440.17672740X-RAY DIFFRACTION95
1.271-1.35060.1741450.17242736X-RAY DIFFRACTION95
1.3506-1.45490.18211410.17062695X-RAY DIFFRACTION95
1.4549-1.60130.15831450.16212740X-RAY DIFFRACTION95
1.6013-1.8330.14361440.1352740X-RAY DIFFRACTION95
1.833-2.30920.15441430.13652725X-RAY DIFFRACTION95
2.3092-27.56090.1791460.10342761X-RAY DIFFRACTION95

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