[English] 日本語
Yorodumi
- PDB-8oly: Structure of Oceanobacillus iheyensis group II intron post first ... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more