[English] 日本語
Yorodumi
- PDB-6t3r: Structure of Oceanobacillus iheyensis group II intron U-mutant (C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t3r
TitleStructure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exon
Components(Group IIC Intron ...) x 2
KeywordsRNA / Ribozyme / Self-splicing / Retrotransposition / Spliceosome
Function / homology: / SPERMINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOceanobacillus iheyensis HTE831 (bacteria)
Oceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.57 Å
AuthorsMarcia, M. / Pyle, A.M.
Funding support France, United States, 3items
OrganizationGrant numberCountry
Other governmentANR-10-INSB-05-02 France
Other governmentANR-10-LABX-49-01 France
Howard Hughes Medical Institute United States
CitationJournal: Nat Commun / Year: 2020
Title: Visualizing group II intron dynamics between the first and second steps of splicing.
Authors: Manigrasso, J. / Chillon, I. / Genna, V. / Vidossich, P. / Somarowthu, S. / Pyle, A.M. / De Vivo, M. / Marcia, M.
History
DepositionOct 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Group IIC Intron Ribozyme
B: Group IIC Intron Ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,24958
Polymers129,1812
Non-polymers3,06856
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-300 kcal/mol
Surface area57230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.458, 95.100, 222.402
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Group IIC Intron ... , 2 types, 2 molecules AB

#1: RNA chain Group IIC Intron Ribozyme


Mass: 126596.945 Da / Num. of mol.: 1 / Fragment: domains 1-5 / Mutation: C289U/C358U/G385A / Source method: obtained synthetically / Details: in vitro transcription system / Source: (synth.) Oceanobacillus iheyensis HTE831 (bacteria)
#2: RNA chain Group IIC Intron Ribozyme


Mass: 2583.569 Da / Num. of mol.: 1 / Fragment: 5'-exon / Source method: obtained synthetically / Details: in vitro transcription system / 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: 3.66 Å3/Da / Density % sol: 66.41 % / Mosaicity: 0.46 °
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM Na-HEPES pH 7.0, 100 mM magnesium acetate, 150 mM potassium chloride, 10 mM lithium chloride, 4% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2013
RadiationMonochromator: SINGLE CRYSTAL SI(220) SIDE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.567→44.48 Å / Num. all: 22945 / Num. obs: 22945 / % possible obs: 98.7 % / Redundancy: 4.7 % / Rpim(I) all: 0.068 / Rrim(I) all: 0.157 / Rsym value: 0.13 / Net I/av σ(I): 4.6 / Net I/σ(I): 9.4 / Num. measured all: 108124
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.57-3.764.80.7980.91602433050.3850.9210.7982.599.3
3.76-3.994.90.5121.31536931540.250.60.5123.699.8
3.99-4.264.90.4261.61451129830.2050.4920.4264.599.6
4.26-4.614.80.2892.31341127690.1430.3390.2896.499.6
4.61-5.054.80.1963.31220525630.0990.2340.1968.999.4
5.05-5.644.70.1215.41080423180.0640.1480.12112.599
5.64-6.514.60.0897.3939020580.0490.1120.08915.798.6
6.51-7.984.40.0688.9762917370.0380.0840.0681998.3
7.98-11.284.40.05510.7600413670.0320.070.0552297.3
11.28-44.4840.04413.627776910.0260.0540.04423.684.8

-
Processing

Software
NameVersionClassification
XDSVERSION March 30, 2013data reduction
SCALA3.3.20data scaling
PHENIX1.14-3260refinement
PDB_EXTRACT3.25data extraction
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IGI

3igi


Resolution: 3.57→34.85 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.1
RfactorNum. reflection% reflection
Rfree0.2504 1175 5.13 %
Rwork0.2119 --
obs0.2138 22894 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 328.26 Å2 / Biso mean: 122.1935 Å2 / Biso min: 50.16 Å2
Refinement stepCycle: final / Resolution: 3.57→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8450 107 49 8606
Biso mean--101.29 97.92 -
Num. residues----394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.57-3.730.33761580.2891267799
3.7297-3.92610.3011600.2487266199
3.9261-4.17170.25971250.24292732100
4.1717-4.49320.30621560.2355271999
4.4932-4.94420.26071520.224271199
4.9442-5.6570.22091470.202271999
5.657-7.11720.24391410.1875274298
7.1172-34.850.21131360.1898275894

+
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