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- PDB-3cjz: Effects of N2,N2-dimethylguanosine on RNA structure and stability... -

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Basic information

Entry
Database: PDB / ID: 3cjz
TitleEffects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m22G:A pairs
ComponentsRNA (5'-R(*GP*GP*AP*CP*GP*(M2G)P*AP*CP*GP*UP*CP*CP*U)-3')
KeywordsRNA / N2 / N2-dimethyl guanosine / X-ray crystal structure / m22G:A pair / rRNA / tRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPallan, P.S. / Kreutz, C. / Bosio, S. / Micura, R. / Egli, M.
CitationJournal: Rna / Year: 2008
Title: Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m2 2G:A pairs.
Authors: Pallan, P.S. / Kreutz, C. / Bosio, S. / Micura, R. / Egli, M.
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 22, 2020Group: Advisory / Database references / Derived calculations
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / struct_ref_seq
Item: _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 ..._ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_struct_assembly_prop.value / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.3Feb 21, 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*AP*CP*GP*(M2G)P*AP*CP*GP*UP*CP*CP*U)-3')
B: RNA (5'-R(*GP*GP*AP*CP*GP*(M2G)P*AP*CP*GP*UP*CP*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)8,4012
Polymers8,4012
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint1 kcal/mol
Surface area4790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.118, 25.970, 45.393
Angle α, β, γ (deg.)90.00, 97.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-171-

HOH

21B-243-

HOH

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Components

#1: RNA chain RNA (5'-R(*GP*GP*AP*CP*GP*(M2G)P*AP*CP*GP*UP*CP*CP*U)-3')


Mass: 4200.595 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2ul droplets containing 0.5mM oligonucleotide, 5% 2-methyl -2,4-pentanediol (MPD), 20mM sodium cacodylate, pH 7.0, 6mM spermine-4HCl, 40mM sodium chloride that were equilibrated against a ...Details: 2ul droplets containing 0.5mM oligonucleotide, 5% 2-methyl -2,4-pentanediol (MPD), 20mM sodium cacodylate, pH 7.0, 6mM spermine-4HCl, 40mM sodium chloride that were equilibrated against a reservoir of 1ml of 35% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 301K
Components of the solutions
IDNameCrystal-IDSol-ID
15% MPD11
2sodium cacodylate11
3spermine-4HCl11
4sodium chloride11
535% MPD12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→44.99 Å / Num. all: 6420 / Num. obs: 6027 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 26.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3539 / Mean I/σ(I) obs: 4.8 / Num. unique all: 661 / % possible all: 81.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data collection
X-GENdata reduction
X-GENdata scaling
MOLREP(CCP4)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A cononical A-RNA dodecamer generated with the program TURBO-FRODO omitting U13 and U26.

Resolution: 1.8→44.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.576 / SU ML: 0.135 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.21
Stereochemistry target values: Standard Refmac parameters and the parameters generated by PRODRG (Schuettelkopf, A. W. and van Aalten, D.M.F. 2004. PRODRG: a tool for high-throughput crystallography ...Stereochemistry target values: Standard Refmac parameters and the parameters generated by PRODRG (Schuettelkopf, A. W. and van Aalten, D.M.F. 2004. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes Acta Crystallogr. D Biol. Crystallogr. 60: 1355-1363.) for the residue M2G.
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27742 582 10.8 %RANDOM
Rwork0.19005 ---
obs0.19938 4816 84.12 %-
all-6420 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.807 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å20 Å20.63 Å2
2--0.18 Å20 Å2
3---1.86 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 556 0 115 671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021620
X-RAY DIFFRACTIONr_bond_other_d0.0020.02222
X-RAY DIFFRACTIONr_angle_refined_deg1.3563.007948
X-RAY DIFFRACTIONr_angle_other_deg1.1243576
X-RAY DIFFRACTIONr_chiral_restr0.0510.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02276
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022
X-RAY DIFFRACTIONr_nbd_refined0.1080.276
X-RAY DIFFRACTIONr_nbd_other0.2490.2276
X-RAY DIFFRACTIONr_nbtor_refined0.2360.2230
X-RAY DIFFRACTIONr_nbtor_other0.0770.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0750.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0840.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.228
X-RAY DIFFRACTIONr_scbond_it1.5823931
X-RAY DIFFRACTIONr_scangle_it1.9934.5948
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 25 -
Rwork0.209 235 -
obs-235 56.16 %
Refinement TLS params.Method: refined / Origin x: 0.1389 Å / Origin y: -1.8722 Å / Origin z: 10.7909 Å
111213212223313233
T-0.0232 Å20.0022 Å20.0009 Å2--0.0549 Å2-0.0114 Å2---0.0589 Å2
L2.0857 °2-0.3434 °20.2795 °2-0.2961 °2-0.2948 °2--0.6885 °2
S-0.0909 Å °0.0157 Å °-0.0475 Å °0.0225 Å °0.0412 Å °-0.0166 Å °-0.0058 Å °0.0232 Å °0.0496 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 131 - 13
2X-RAY DIFFRACTION1BB14 - 261 - 13

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