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- PDB-8ruk: Structure of Oceanobacillus iheyensis group II intron in the pres... -

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Basic information

Entry
Database: PDB / ID: 8ruk
TitleStructure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+, and ARN25850
ComponentsDomains 1-5
KeywordsRNA / RIBOZYME / METALLOENZYME / SELF-SPLICING / RETROTRANSPOSITION
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.81 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
DepositionJan 31, 2024Deposition 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: Domains 1-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,89516
Polymers127,9921
Non-polymers90315
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-108 kcal/mol
Surface area58240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.845, 95.144, 225.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain Domains 1-5


Mass: 127991.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis (bacteria)
#2: Chemical ChemComp-VTR / 2-[2,6-bis(bromanyl)-3,4,5-tris(oxidanyl)phenyl]carbonyl-~{N}-(2-pyrrolidin-1-ylethyl)-1-benzofuran-5-carboxamide


Mass: 568.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20Br2N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: 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: 3.72 Å3/Da / Density % sol: 66.97 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM Mg-Acetate, 150 mM NaCl, 50 mM Na-HEPES pH 7.0, 3%PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 4.81→48.55 Å / Num. obs: 9771 / % possible obs: 99.79 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1403 / Net I/σ(I): 12.14
Reflection shellResolution: 4.81→4.982 Å / Num. unique obs: 947 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.81→48.55 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 166.707 / SU ML: 0.904 / Cross valid method: THROUGHOUT / ESU R Free: 1.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24273 508 5.2 %RANDOM
Rwork0.19089 ---
obs0.19385 9286 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 168.148 Å2
Baniso -1Baniso -2Baniso -3
1-12.26 Å20 Å2-0 Å2
2---19.35 Å2-0 Å2
3---7.09 Å2
Refinement stepCycle: 1 / Resolution: 4.81→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8270 46 8 8324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0119315
X-RAY DIFFRACTIONr_bond_other_d0.0020.0193788
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.84514498
X-RAY DIFFRACTIONr_angle_other_deg0.4851.6669207
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_restr0.0530.21929
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021451
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_it6.67610.2479315
X-RAY DIFFRACTIONr_scbond_other6.67610.2479314
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.02518.58414499
X-RAY DIFFRACTIONr_long_range_B_refined17.948127.813594
X-RAY DIFFRACTIONr_long_range_B_other17.948127.8113595
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.81→4.931 Å
RfactorNum. reflection% reflection
Rfree0.333 44 -
Rwork0.216 652 -
obs--99.86 %
Refinement TLS params.Method: refined / Origin x: 23.516 Å / Origin y: 8.4 Å / Origin z: 25.481 Å
111213212223313233
T0.3436 Å2-0.0303 Å20.0785 Å2-1.2822 Å20.0644 Å2--0.2469 Å2
L0.7251 °2-1.206 °2-0.9221 °2-2.3718 °21.4535 °2--1.2806 °2
S-0.378 Å °-0.3644 Å °-0.1241 Å °0.8403 Å °0.1916 Å °0.1512 Å °0.4067 Å °0.3098 Å °0.1863 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 390
2X-RAY DIFFRACTION1A401

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