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

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Basic information

Entry
Database: PDB / ID: 8ruj
TitleStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soaking
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: 3.12 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 30, 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)128,73941
Polymers126,9561
Non-polymers1,78240
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-194 kcal/mol
Surface area56950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.570, 95.098, 227.801
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: 126956.180 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.: 21 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.82 Å3/Da / Density % sol: 67.81 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM magnesium acetate, 200 mM potassium chloride, 10 mM lithium chloride, 50 mM HEPES sodium, pH 7.0, 3% PEG8000

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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 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.12→49.52 Å / Num. obs: 35276 / % possible obs: 98.96 % / Redundancy: 13.5 % / CC1/2: 0.998 / Net I/σ(I): 11.9
Reflection shellResolution: 3.12→3.236 Å / Num. unique obs: 3419 / CC1/2: 0.316

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→49.52 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.975 / SU B: 61.955 / SU ML: 0.453 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23617 1768 5 %RANDOM
Rwork0.19604 ---
obs0.19805 33507 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: 147.217 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å2-0 Å20 Å2
2--8.17 Å2-0 Å2
3----7.39 Å2
Refinement stepCycle: 1 / Resolution: 3.12→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8349 71 63 8483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0119440
X-RAY DIFFRACTIONr_bond_other_d0.0020.0193825
X-RAY DIFFRACTIONr_angle_refined_deg2.4721.84414644
X-RAY DIFFRACTIONr_angle_other_deg0.6741.6659292
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_restr0.0890.21945
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024701
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021470
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_it8.3528.319440
X-RAY DIFFRACTIONr_scbond_other8.3528.319441
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.66314.97614645
X-RAY DIFFRACTIONr_long_range_B_refined15.565104.9814022
X-RAY DIFFRACTIONr_long_range_B_other15.565104.9914023
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.124→3.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 114 -
Rwork0.397 2412 -
obs--98.71 %
Refinement TLS params.Method: refined / Origin x: -24.6245 Å / Origin y: 8.7639 Å / Origin z: -25.9251 Å
111213212223313233
T0.8088 Å2-0.0437 Å2-0.0091 Å2-0.0972 Å20.0027 Å2--0.9495 Å2
L0.7665 °20.4829 °2-1.0753 °2-1.3303 °2-0.7945 °2--1.7524 °2
S-0.1208 Å °0.244 Å °-0.1678 Å °-0.3893 Å °0.0984 Å °-0.0654 Å °0.1906 Å °-0.3012 Å °0.0224 Å °

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