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- PDB-8sx5: GpppA dinucleotide binding to RNA CU template -

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Basic information

Entry
Database: PDB / ID: 8sx5
TitleGpppA dinucleotide binding to RNA CU template
ComponentsRNA (5'-R(*(TLN)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: 1.95 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 19, 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(*(TLN)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GA3))-3')
B: RNA (5'-R(*(TLN)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)10,5724
Polymers9,0282
Non-polymers1,5452
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint8 kcal/mol
Surface area5570 Å2
Unit cell
Length a, b, c (Å)44.522, 44.522, 85.524
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
11B-206-

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*(GA3))-3')


Mass: 4513.789 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) 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.: 8 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05 M magnesium sulfate hydrate, 0.05 M HEPES sodium, pH 7.0, 1.6 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: 0.987 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: 1.95→50 Å / Num. obs: 6922 / % possible obs: 100 % / Redundancy: 8.9 % / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.052 / Rrim(I) all: 0.148 / Χ2: 1.168 / Net I/σ(I): 10
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 13.5 / Num. unique obs: 756 / CC1/2: 0.972 / CC star: 0.993 / Rpim(I) all: 0.143 / Rrim(I) all: 0.438 / Χ2: 1.25 / % possible all: 90.8

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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 6C8K

6c8k


Resolution: 1.95→28.52 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.829 / SU B: 4.478 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32316 301 4.4 %RANDOM
Rwork0.28399 ---
obs0.28576 6597 90.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.942 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.95→28.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 598 100 8 706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.017780
X-RAY DIFFRACTIONr_bond_other_d0.0230.024346
X-RAY DIFFRACTIONr_angle_refined_deg3.6882.0121222
X-RAY DIFFRACTIONr_angle_other_deg3.7613.109824
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_restr0.2470.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021134
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_it2.2972.823780
X-RAY DIFFRACTIONr_scbond_other2.2952.822781
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9894.2361223
X-RAY DIFFRACTIONr_long_range_B_refined4.07725.999996
X-RAY DIFFRACTIONr_long_range_B_other4.07526.012997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 31 -
Rwork0.195 518 -
obs--98.39 %

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