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- PDB-6vem: Structure of RNA octamer -

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Basic information

Entry
Database: PDB / ID: 6vem
TitleStructure of RNA octamer
ComponentsModified Octamer RNA
KeywordsRNA / Synthetic RNA / 5'-C-Metyl-guanosine
Function / homologyCOBALT HEXAMMINE(III) / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Synthesis, chirality-dependent conformational and biological properties of siRNAs containing 5'-(R)- and 5'-(S)-C-methyl-guanosine.
Authors: Mikami, A. / Erande, N. / Matsuda, S. / Kel'in, A. / Woods, L.B. / Chickering, T. / Pallan, P.S. / Schlegel, M.K. / Zlatev, I. / Egli, M. / Manoharan, M.
History
DepositionJan 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Modified Octamer RNA
B: Modified Octamer RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9477
Polymers5,1412
Non-polymers8065
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-7 kcal/mol
Surface area3200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.921, 37.921, 57.852
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: RNA chain Modified Octamer RNA


Mass: 2570.619 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: GMX is 5 prime-C-methyl-guanosine / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Sodium cacodylate (20 mM, pH 6.0), sodium chloride (40 mM), hexamine cobalt(III) chloride (10 mM), and 2-methyl-2,4-pentanediol (MPD; 5% (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9183 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 2, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 1.56→23 Å / Num. obs: 6721 / % possible obs: 99.3 % / Redundancy: 18.5 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.015 / Net I/av σ(I): 63.3 / Net I/σ(I): 63.32
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.869 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 627 / Rpim(I) all: 0.243 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPCCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 259D

259d


Resolution: 1.56→21.72 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 5.046 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.098
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 295 4.4 %RANDOM
Rwork0.1775 ---
obs0.1799 6392 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.43 Å2 / Biso mean: 38.293 Å2 / Biso min: 20.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 1.56→21.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 340 35 30 405
Biso mean--37.26 49.89 -
Num. residues----16
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.013408
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.66663
X-RAY DIFFRACTIONr_chiral_restr0.1050.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0290.02168
X-RAY DIFFRACTIONr_rigid_bond_restr7.6743408
LS refinement shellResolution: 1.562→1.602 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 24 -
Rwork0.259 426 -
all-450 -
obs--92.4 %

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