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- PDB-8swg: RNA duplex bound with GpppA dinucleotide ligand -

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Basic information

Entry
Database: PDB / ID: 8swg
TitleRNA duplex bound with GpppA dinucleotide ligand
ComponentsRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GA3))-3')
KeywordsRNA / GpppA
Function / homologyGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 18, 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

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Assembly

Deposited unit
A: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GA3))-3')
B: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GA3))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5704
Polymers9,0262
Non-polymers1,5452
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint1 kcal/mol
Surface area5610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.543, 43.543, 84.269
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-216-

HOH

21A-221-

HOH

31A-231-

HOH

41B-205-

HOH

51B-224-

HOH

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Components

#1: RNA chain RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GA3))-3')


Mass: 4512.804 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Chemical ChemComp-G3A / GUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE


Mass: 772.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H27N10O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris, pH 6.5, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 15337 / % possible obs: 99.8 % / Redundancy: 10.2 % / CC1/2: 0.966 / CC star: 0.991 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.029 / Rrim(I) all: 0.089 / Χ2: 1.714 / Net I/σ(I): 21.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 8 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1506 / CC1/2: 0.969 / CC star: 0.992 / Rpim(I) all: 0.212 / Rrim(I) all: 0.603 / Χ2: 1.104 / % 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 5HBX

5hbx


Resolution: 1.5→37.74 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.389 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26634 707 4.7 %RANDOM
Rwork0.21798 ---
obs0.22029 14486 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.183 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.5→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 698 0 55 753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.017782
X-RAY DIFFRACTIONr_bond_other_d0.0230.024356
X-RAY DIFFRACTIONr_angle_refined_deg3.2542.011224
X-RAY DIFFRACTIONr_angle_other_deg3.6643.115832
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_restr0.4310.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.021386
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022136
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_it2.4272.773782
X-RAY DIFFRACTIONr_scbond_other2.4262.774783
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4414.191225
X-RAY DIFFRACTIONr_long_range_B_refined4.23526.951054
X-RAY DIFFRACTIONr_long_range_B_other4.23326.8791051
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 53 -
Rwork0.255 1016 -
obs--98.8 %

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