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- PDB-5lqo: RNA duplex has central consecutive GA pairs flanked by G-C basepairs -

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Basic information

Entry
Database: PDB / ID: 5lqo
TitleRNA duplex has central consecutive GA pairs flanked by G-C basepairs
ComponentsRNA (5'-R(*GP*(CBV)P*CP*GP*GP*AP*CP*GP*GP*C)-3')
KeywordsRNA / N6-methyladenine / RNA folding / Watson-Crick basepairs
Function / homologyRNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: EMBO Rep. / Year: 2017
Title: Control of box C/D snoRNP assembly by N(6)-methylation of adenine.
Authors: Huang, L. / Ashraf, S. / Wang, J. / Lilley, D.M.
History
DepositionAug 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*(CBV)P*CP*GP*GP*AP*CP*GP*GP*C)-3')
B: RNA (5'-R(*GP*(CBV)P*CP*GP*GP*AP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,6202
Polymers6,6202
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-0 kcal/mol
Surface area3530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.469, 33.469, 113.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: RNA chain RNA (5'-R(*GP*(CBV)P*CP*GP*GP*AP*CP*GP*GP*C)-3')


Mass: 3309.900 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.025 M Magnesium Sulfate, 0.05 M Tris Hydrochloride pH 8.5, 1.8 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9196 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 1.87→33.47 Å / Num. obs: 5917 / % possible obs: 100 % / Observed criterion σ(I): 1.3 / Redundancy: 12.2 % / CC1/2: 1 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.7
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 13 % / Rmerge(I) obs: 2.08 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.446 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→32.108 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 47.85
RfactorNum. reflection% reflection
Rfree0.2556 477 4.87 %
Rwork0.2456 --
obs0.2461 5654 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.87→32.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 432 0 20 452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005482
X-RAY DIFFRACTIONf_angle_d1.458754
X-RAY DIFFRACTIONf_dihedral_angle_d11.11216
X-RAY DIFFRACTIONf_chiral_restr0.0496
X-RAY DIFFRACTIONf_plane_restr0.00620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8702-2.14080.45011350.42053066X-RAY DIFFRACTION94
2.1408-2.69690.37761680.36043151X-RAY DIFFRACTION98
2.6969-32.11290.21591740.19293098X-RAY DIFFRACTION96
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)
16.2066-0.55234.57730.55720.29224.4375-0.0001-0.2765-0.2030.02560.12480.1756-0.6674-0.2444-0.18860.3622-0.0550.06880.4371-0.03330.3512-19.3608-5.3736-6.5122
20.5559-0.7945-0.55568.08035.3793.564-0.2083-0.31690.63660.38230.26590.0439-0.360.1999-0.08120.4977-0.0341-0.04520.2947-0.07240.4125-9.69511.10846.5802
33.7416-1.5494-4.61393.78530.86018.55620.12130.86860.4086-0.28430.1194-0.01980.0935-1.4594-0.21230.5327-0.0651-0.0890.5690.0870.4245-16.19374.44632.0926
47.85141.91541.60369.27792.21177.50330.2840.5380.1864-1.0719-0.55910.4815-0.2598-0.12450.2840.3310.1105-0.00550.46160.02050.2923-13.3101-7.3092-11.2635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:6)
2X-RAY DIFFRACTION2(chain A and resid 7:10)
3X-RAY DIFFRACTION3(chain B and resid 1:5)
4X-RAY DIFFRACTION4(chain B and resid 6:10)

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