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- PDB-8oly: Structure of Oceanobacillus iheyensis group II intron post first ... -

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Basic information

Entry
Database: PDB / ID: 8oly
TitleStructure of Oceanobacillus iheyensis group II intron post first step of splicing in the presence of K+, Mg2+ and intronistat B
Components
  • 5'-exon
  • Group IIC intron
KeywordsRNA / RIBOZYME / METALLOENZYME / SELF-SPLICING / RETROTRANSPOSITION
Function / homology: / SPERMINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsSilvestri, I. / Marcia, M.
Funding support France, Italy, 8items
OrganizationGrant numberCountry
Other governmentITMO Cancer 18CN047-00
Other governmentR21105CC
Other privateFINOVI AAP15
Other governmentCanceropole CLARA Oncostarter
Fondation ARCPJA-20191209284 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-02 France
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)ANR-10-LABX-49-01 France
Italian Association for Cancer ResearchIG 23679 Italy
CitationJournal: Nat Commun / Year: 2024
Title: Targeting the conserved active site of splicing machines with specific and selective small molecule modulators.
Authors: Silvestri, I. / Manigrasso, J. / Andreani, A. / Brindani, N. / Mas, C. / Reiser, J.B. / Vidossich, P. / Martino, G. / McCarthy, A.A. / De Vivo, M. / Marcia, M.
History
DepositionMar 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Group IIC intron
B: 5'-exon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,57258
Polymers128,5042
Non-polymers3,06856
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-298 kcal/mol
Surface area56730 Å2
Unit cell
Length a, b, c (Å)88.518, 94.686, 222.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain Group IIC intron


Mass: 126956.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis (bacteria)
#2: RNA chain 5'-exon


Mass: 1547.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis (bacteria)

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Non-polymers , 5 types, 105 molecules

#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.63 Å3/Da / Density % sol: 66.15 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM magnesium acetate, 100 mM potassium chloride, 10 mM lithium chloride, 50 mM HEPES sodium, pH 7.0, 3.5% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 3.1→48.02 Å / Num. obs: 34101 / % possible obs: 98.69 % / Redundancy: 4.2 % / CC1/2: 1 / Net I/σ(I): 10.57
Reflection shellResolution: 3.1→3.2 Å / Num. unique obs: 3245 / CC1/2: 0.22

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→48.02 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.956 / SU B: 23.462 / SU ML: 0.375 / Cross valid method: THROUGHOUT / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23712 1616 4.7 %RANDOM
Rwork0.19964 ---
obs0.20146 32471 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.16 Å2-0 Å20 Å2
2---3.76 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 3.11→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8475 107 49 8631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0119643
X-RAY DIFFRACTIONr_bond_other_d0.0030.023928
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.41914870
X-RAY DIFFRACTIONr_angle_other_deg1.3612.5879530
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_restr0.0940.21576
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021876
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_it11.37914.5479643
X-RAY DIFFRACTIONr_scbond_other11.37514.5469642
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.58821.82214871
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.111→3.192 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 107 -
Rwork0.391 2263 -
obs--93.86 %

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