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- PDB-6z18: Crystal structure of RNA-10mer: CCGG(N4,N4-dimethyl-C)GCCGG; R32 form -

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Basic information

Entry
Database: PDB / ID: 6z18
TitleCrystal structure of RNA-10mer: CCGG(N4,N4-dimethyl-C)GCCGG; R32 form
ComponentsRNA-10mer: CCGG(N4,N4-dimethyl-C)GCCGG
KeywordsRNA / RNA DUPLEX 10MER / N4 / N4-dimethylcytidine
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsRuszkowski, M. / Sekula, B. / Mao, S. / Haruehanroengra, P. / Sheng, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1845486 United States
National Science Foundation (NSF, United States)MCB-1715234 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Base pairing, structural and functional insights into N4-methylcytidine (m4C) and N4,N4-dimethylcytidine (m42C) modified RNA.
Authors: Mao, S. / Sekula, B. / Ruszkowski, M. / Ranganathan, S.V. / Haruehanroengra, P. / Wu, Y. / Shen, F. / Sheng, J.
History
DepositionMay 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2May 1, 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

Downloads & links

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Assembly

Deposited unit
A: RNA-10mer: CCGG(N4,N4-dimethyl-C)GCCGG
B: RNA-10mer: CCGG(N4,N4-dimethyl-C)GCCGG


Theoretical massNumber of molelcules
Total (without water)6,4702
Polymers6,4702
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-3 kcal/mol
Surface area3840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.562, 42.562, 165.919
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: RNA chain RNA-10mer: CCGG(N4,N4-dimethyl-C)GCCGG


Mass: 3235.033 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040 M Sodium cacodylate trihydrate pH 6.0, 0.012 M Spermine tetrahydrochloride, 0.012 M Sodium chloride, and 0.080 M Potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→36 Å / Num. obs: 2771 / % possible obs: 85.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 26.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.4
Reflection shellResolution: 1.81→1.99 Å / Rmerge(I) obs: 1.43 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 231 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
XDSdata reduction
STARANISOdata scaling
PHASERphasing
PHENIX1.18.1_3865refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CCGGCGCCGG dimer

Resolution: 1.81→35.98 Å / SU ML: 0.2079 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.7659
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.288 149 5.42 %
Rwork0.2537 2599 -
obs0.2558 2748 48.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.78 Å2
Refinement stepCycle: LAST / Resolution: 1.81→35.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 428 0 3 431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061476
X-RAY DIFFRACTIONf_angle_d1.116740
X-RAY DIFFRACTIONf_chiral_restr0.041996
X-RAY DIFFRACTIONf_plane_restr0.005722
X-RAY DIFFRACTIONf_dihedral_angle_d10.4353234
LS refinement shellResolution: 1.81→35.98 Å
RfactorNum. reflection% reflection
Rfree0.288 149 -
Rwork0.2537 2599 -
obs--48.75 %
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)
11.91535364467-0.1581649679041.332164015151.575563478211.278588500332.162303053410.24017658809-0.474459309726-0.4571583576990.871195658955-0.02301686371690.1871316557260.1827651238920.133830232429-0.02039318390610.588384191957-0.130342553831-0.02983820313060.386688338180.07870845572880.227362830865-3.8373058380813.747410138115.3605942691
21.59339457229-0.226249145068-1.116317572380.1251234260950.7045958606124.015382767930.1096006007790.00588278504236-0.3809201298540.631826856294-0.00450617376919-0.2031287581930.53905549831-0.489940946833-0.04409527282560.757689513332-0.0431615014772-0.1291392245220.4369400449150.0400186428620.325319729684-5.8417734474613.643820497711.110098196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )AA - B1 - 10
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 10 )BC1 - 10

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