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- PDB-8clm: 1.80 A crystal structure of RNA/2'-O-methyl-RNA heteroduplex -

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Basic information

Entry
Database: PDB / ID: 8clm
Title1.80 A crystal structure of RNA/2'-O-methyl-RNA heteroduplex
Components
  • RNA (5'-R(*(UZL)*(OMU)P*(A2M)P*(OMG)P*(OMG)P*(A2M)P*(OMG)P*(A2M)P*(OMC)P*)-3')
  • RNA (5'-R(*G*UP*CP*UP*CP*CP*UP*AP*GP*)-3')
KeywordsRNA / RNA/2'-OMeRNA heteroduplex
Function / homology: / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDolot, R.M. / Maciaszek, A. / Nawrot, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of RNA/2'-O-methyl-RNA heteroduplex
Authors: Dolot, R.M. / Maciaszek, A. / Mikolajczyk, B. / Nawrot, B.C.
History
DepositionFeb 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*G*UP*CP*UP*CP*CP*UP*AP*GP*)-3')
D: RNA (5'-R(*(UZL)*(OMU)P*(A2M)P*(OMG)P*(OMG)P*(A2M)P*(OMG)P*(A2M)P*(OMC)P*)-3')
B: RNA (5'-R(*G*UP*CP*UP*CP*CP*UP*AP*GP*)-3')
E: RNA (5'-R(*(UZL)*(OMU)P*(A2M)P*(OMG)P*(OMG)P*(A2M)P*(OMG)P*(A2M)P*(OMC)P*)-3')
C: RNA (5'-R(*G*UP*CP*UP*CP*CP*UP*AP*GP*)-3')
F: RNA (5'-R(*(UZL)*(OMU)P*(A2M)P*(OMG)P*(OMG)P*(A2M)P*(OMG)P*(A2M)P*(OMC)P*)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3848
Polymers17,2496
Non-polymers1352
Water5,693316
1
A: RNA (5'-R(*G*UP*CP*UP*CP*CP*UP*AP*GP*)-3')
D: RNA (5'-R(*(UZL)*(OMU)P*(A2M)P*(OMG)P*(OMG)P*(A2M)P*(OMG)P*(A2M)P*(OMC)P*)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8854
Polymers5,7502
Non-polymers1352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (5'-R(*G*UP*CP*UP*CP*CP*UP*AP*GP*)-3')
E: RNA (5'-R(*(UZL)*(OMU)P*(A2M)P*(OMG)P*(OMG)P*(A2M)P*(OMG)P*(A2M)P*(OMC)P*)-3')


Theoretical massNumber of molelcules
Total (without water)5,7502
Polymers5,7502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (5'-R(*G*UP*CP*UP*CP*CP*UP*AP*GP*)-3')
F: RNA (5'-R(*(UZL)*(OMU)P*(A2M)P*(OMG)P*(OMG)P*(A2M)P*(OMG)P*(A2M)P*(OMC)P*)-3')


Theoretical massNumber of molelcules
Total (without water)5,7502
Polymers5,7502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.103, 49.303, 55.868
Angle α, β, γ (deg.)90.000, 97.149, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 2808.703 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(*(UZL)*(OMU)P*(A2M)P*(OMG)P*(OMG)P*(A2M)P*(OMG)P*(A2M)P*(OMC)P*)-3')


Mass: 2941.065 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 46.06 % / Description: prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 mM duplex, 1.4 M Li2SO4, 50 mM sodium cacodylate, 1 mM spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.8→19.011 Å / Num. obs: 15124 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 8.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.046 / Rrim(I) all: 0.094 / Χ2: 0.99 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 868 / CC1/2: 0.817 / Rpim(I) all: 0.382 / Rrim(I) all: 0.747 / Χ2: 1.01 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
CrysalisPro41.100adata reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.011 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.644 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.151
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2561 723 4.795 %
Rwork0.188 14354 -
all0.191 --
obs-15077 99.413 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.582 Å2
Baniso -1Baniso -2Baniso -3
1--1.766 Å20 Å20.125 Å2
2---0.416 Å2-0 Å2
3---2.085 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1158 6 316 1480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0111291
X-RAY DIFFRACTIONr_bond_other_d0.0020.018609
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.8321986
X-RAY DIFFRACTIONr_angle_other_deg0.5021.6541446
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.189539
X-RAY DIFFRACTIONr_chiral_restr0.090.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02639
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02204
X-RAY DIFFRACTIONr_nbd_refined0.1170.2172
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.2697
X-RAY DIFFRACTIONr_nbtor_refined0.240.2488
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1050.2358
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2216
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2230.213
X-RAY DIFFRACTIONr_nbd_other0.1780.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.228
X-RAY DIFFRACTIONr_scbond_it2.4293.4581291
X-RAY DIFFRACTIONr_scbond_other2.3993.4561285
X-RAY DIFFRACTIONr_scangle_it3.5696.2841986
X-RAY DIFFRACTIONr_scangle_other3.5226.2821981
X-RAY DIFFRACTIONr_lrange_it6.35349.6461940
X-RAY DIFFRACTIONr_lrange_other5.96347.0811829
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8460.377580.25910170.26510750.920.9441000.216
1.846-1.8960.241620.23710330.23710950.960.9561000.203
1.896-1.9510.226630.2189650.21810280.9580.961000.18
1.951-2.010.255470.2279970.22810440.9540.961000.192
2.01-2.0750.254320.2069590.2089910.950.9671000.172
2.075-2.1470.276320.2059360.2079680.9460.9711000.177
2.147-2.2270.223470.198750.1929220.9620.9751000.16
2.227-2.3170.327480.1938420.2018910.930.97499.88780.162
2.317-2.4180.362390.2067930.2138330.9160.97499.880.169
2.418-2.5340.283400.217850.2148260.9490.97499.87890.178
2.534-2.6690.263400.2127330.2147750.960.97199.74190.18
2.669-2.8270.363340.2336860.2397270.9350.96799.03710.205
2.827-3.0180.316300.1826780.1887160.9480.98198.88270.167
3.018-3.2520.228270.1626070.1656370.9790.98999.5290.16
3.252-3.5530.199310.1525800.1546160.9790.98999.18830.15
3.553-3.9550.165190.1365250.1375510.990.99198.72960.143
3.955-4.5340.268240.1644490.174850.9560.98597.52580.165
4.534-5.4750.167190.1763890.1754160.9830.98598.07690.18
5.475-7.4410.289210.1873140.1943420.9660.98397.95320.191
7.441-19.0110.207100.1841910.1852130.9810.9894.36620.192

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