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- PDB-8sy1: RNA duplex bound with imidazolium bridged GA dinucleotide -

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Basic information

Entry
Database: PDB / ID: 8sy1
TitleRNA duplex bound with imidazolium bridged GA dinucleotide
ComponentsRNA (5'-R(*(TLN)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GMA))-3')
KeywordsRNA / imidazolium bridged GA dinucleotide
Function / homologyChem-WZW / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsZhang, W. / Dantsu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Chem Biol / Year: 2023
Title: Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand.
Authors: Dantsu, Y. / Zhang, Y. / Zhang, W.
History
DepositionMay 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 1.2Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*(TLN)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GMA))-3')
B: RNA (5'-R(*(TLN)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GMA))-3')
C: RNA (5'-R(*(TLN)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GMA))-3')
D: RNA (5'-R(*(TLN)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GMA))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0898
Polymers18,0554
Non-polymers3,0344
Water1,00956
1
A: RNA (5'-R(*(TLN)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GMA))-3')
B: RNA (5'-R(*(TLN)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GMA))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5454
Polymers9,0282
Non-polymers1,5172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint11 kcal/mol
Surface area5700 Å2
MethodPISA
2
C: RNA (5'-R(*(TLN)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GMA))-3')
D: RNA (5'-R(*(TLN)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GMA))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5454
Polymers9,0282
Non-polymers1,5172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint13 kcal/mol
Surface area5590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.656, 43.656, 81.126
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-103-

HOH

21A-105-

HOH

31A-108-

HOH

41B-203-

HOH

51B-206-

HOH

61C-207-

HOH

71C-213-

HOH

81C-218-

HOH

91C-220-

HOH

101D-208-

HOH

111D-211-

HOH

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Components

#1: RNA chain
RNA (5'-R(*(TLN)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GMA))-3')


Mass: 4513.789 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) synthetic construct (others)
#2: Chemical
ChemComp-WZW / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-[2-azanyl-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]imidazol-1-yl]phosphinic acid


Mass: 758.511 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H30N13O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 1.0 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 15744 / % possible obs: 91.9 % / Redundancy: 5.5 % / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.104 / Χ2: 1.256 / Net I/σ(I): 19.6
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1726 / CC1/2: 0.825 / CC star: 0.951 / Rrim(I) all: 0.638 / Χ2: 0.644 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8SWG

8swg


Resolution: 1.76→34.29 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.092 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25633 795 5.1 %RANDOM
Rwork0.22375 ---
obs0.22543 14945 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.779 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.76→34.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1196 148 56 1400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0171508
X-RAY DIFFRACTIONr_bond_other_d0.0230.024692
X-RAY DIFFRACTIONr_angle_refined_deg2.8371.9862356
X-RAY DIFFRACTIONr_angle_other_deg3.8263.0971622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1410.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021754
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022268
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5852.7371508
X-RAY DIFFRACTIONr_scbond_other2.5632.7361505
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3224.1022354
X-RAY DIFFRACTIONr_long_range_B_refined4.526.8332091
X-RAY DIFFRACTIONr_long_range_B_other4.526.8322091
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.761→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 99 -
Rwork0.119 1187 -
obs--98.62 %

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