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

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Basic information

Entry
Database: PDB / ID: 8ruh
TitleStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exon
Components
  • 5'-exon
  • Domains 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: 4.55 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

Downloads & links

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Assembly

Deposited unit
A: Domains 1-5
B: 5'-exon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,65550
Polymers128,7942
Non-polymers1,86148
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-265 kcal/mol
Surface area57860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.204, 96.484, 231.693
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 Domains 1-5


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


Mass: 1838.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis (bacteria)

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Non-polymers , 4 types, 93 molecules

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


Mass: 24.305 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 18 / 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.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.91 Å3/Da / Density % sol: 68.58 %
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, 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: Dec 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 4.55→89.23 Å / Num. obs: 12132 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0545 / Net I/σ(I): 11.08
Reflection shellResolution: 4.55→4.713 Å / Rmerge(I) obs: 1.301 / Num. unique obs: 1156 / CC1/2: 0.573

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.55→89.23 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 69 / SU ML: 0.827 / Cross valid method: THROUGHOUT / ESU R Free: 1.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25782 620 5.1 %RANDOM
Rwork0.1844 ---
obs0.18835 11512 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 204.015 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å2-0 Å20 Å2
2---10.77 Å20 Å2
3---9.6 Å2
Refinement stepCycle: 1 / Resolution: 4.55→89.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8440 62 45 8547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0119529
X-RAY DIFFRACTIONr_bond_other_d0.0020.0193861
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.83914769
X-RAY DIFFRACTIONr_angle_other_deg0.4071.6599377
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_restr0.0480.21965
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021487
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_it15.5321.3279529
X-RAY DIFFRACTIONr_scbond_other15.52921.3279530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other24.76638.64914770
X-RAY DIFFRACTIONr_long_range_B_refined35.433271.2813799
X-RAY DIFFRACTIONr_long_range_B_other35.432271.2813800
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.55→4.667 Å
RfactorNum. reflection% reflection
Rfree0.327 44 -
Rwork0.242 799 -
obs--98.02 %

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