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- PDB-5lr5: N6-methyladenine is accommodated in a conventional A-U basepair -

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Basic information

Entry
Database: PDB / ID: 5lr5
TitleN6-methyladenine is accommodated in a conventional A-U basepair
ComponentsRNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*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: 2.4 Å
AuthorsHuang, L. / Lilley, D.M.J.
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 18, 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 2.0Feb 20, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_seq_map_depositor_info / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2May 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*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
B: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
C: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
D: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1765
Polymers13,0794
Non-polymers961
Water18010
1
A: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
B: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,5402
Polymers6,5402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint5 kcal/mol
Surface area3230 Å2
MethodPISA
2
C: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
D: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6363
Polymers6,5402
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-12 kcal/mol
Surface area3220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.470, 50.470, 108.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: RNA chain
RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')


Mass: 3269.872 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Sulfate 0.1 M Sodium Acetate trihydrate pH 4.6 25% w/v Polyethylene Glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9193 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9193 Å / Relative weight: 1
ReflectionResolution: 2.27→43.71 Å / Num. obs: 5911 / % possible obs: 98.4 % / Observed criterion σ(I): 1.4 / Redundancy: 41.7 % / CC1/2: 1 / Rmerge(I) obs: 0.143 / Net I/σ(I): 13.3
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 38.7 % / Rmerge(I) obs: 2.7 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.545 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→43.708 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.71
RfactorNum. reflection% reflection
Rfree0.2873 528 4.54 %
Rwork0.2474 --
obs0.249 5910 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→43.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 856 5 10 871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02956
X-RAY DIFFRACTIONf_angle_d4.6911494
X-RAY DIFFRACTIONf_dihedral_angle_d10.504404
X-RAY DIFFRACTIONf_chiral_restr0.053188
X-RAY DIFFRACTIONf_plane_restr0.00340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.64160.43581200.42352802X-RAY DIFFRACTION96
2.6416-3.02370.41421820.38582765X-RAY DIFFRACTION98
3.0237-3.80930.2831050.28472677X-RAY DIFFRACTION92
3.8093-43.71550.21771210.1722865X-RAY DIFFRACTION99

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