[English] 日本語
Yorodumi
- PDB-3eog: Co-crystallization showing exon recognition by a group II intron -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eog
TitleCo-crystallization showing exon recognition by a group II intron
Components
  • 5'-R(*UP*UP*AP*UP*UP*A)-3'
  • Group IIC intron
KeywordsRNA / Ribonucleic acid / Intron / Group II / exon
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.391 Å
AuthorsToor, N. / Rajashankar, K. / Keating, K.S. / Pyle, A.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis for exon recognition by a group II intron.
Authors: Toor, N. / Rajashankar, K. / Keating, K.S. / Pyle, A.M.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Group IIC intron
B: 5'-R(*UP*UP*AP*UP*UP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,67444
Polymers135,4902
Non-polymers1,18442
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-269 kcal/mol
Surface area57320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.485, 95.078, 225.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: RNA chain Group IIC intron


Mass: 133652.156 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Oceanobacillus iheyensis sequence modified using PCR mutagenesis
#2: RNA chain 5'-R(*UP*UP*AP*UP*UP*A)-3'


Mass: 1838.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Ligated exon construct
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growTemperature: 303 K / pH: 7
Details: 6% PEG 3350, 150 mM magnesium acetate, 350 mM KCL, 50 mM Na-HEPES pH 7.0, 0.5 mM spermine, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2magnesium acetate11
3KCL11
4Na-HEPES11
5spermine11
6PEG 335012
7magnesium acetate12
8KCL12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2008
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.391→48.6 Å / Num. obs: 27468

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.391→48.419 Å / SU ML: 0.52 / σ(F): 0.21 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 1312 5.02 %
Rwork0.2077 --
obs0.2105 26156 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.958 Å2 / ksol: 0.173 e/Å3
Refinement stepCycle: LAST / Resolution: 3.391→48.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8396 42 15 8453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049405
X-RAY DIFFRACTIONf_angle_d1.48814667
X-RAY DIFFRACTIONf_dihedral_angle_d28.8995439
X-RAY DIFFRACTIONf_chiral_restr0.0781959
X-RAY DIFFRACTIONf_plane_restr0.005388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.391-3.52670.32581330.26292505X-RAY DIFFRACTION90
3.5267-3.68720.26611390.24122656X-RAY DIFFRACTION94
3.6872-3.88150.27971440.20572679X-RAY DIFFRACTION96
3.8815-4.12460.25611420.20272725X-RAY DIFFRACTION97
4.1246-4.44280.24541470.19772765X-RAY DIFFRACTION98
4.4428-4.88950.23911480.18742809X-RAY DIFFRACTION99
4.8895-5.59620.22561490.17472849X-RAY DIFFRACTION99
5.5962-7.04710.26531520.18762879X-RAY DIFFRACTION100
7.0471-48.42380.27421580.22572977X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 19.2473 Å / Origin y: 86.149 Å / Origin z: 363.1506 Å
111213212223313233
T0.6481 Å20.0114 Å2-0.0286 Å2-0.5989 Å2-0.077 Å2--0.5729 Å2
L0.454 °2-0.2826 °20.4671 °2-0.5886 °2-0.4532 °2--0.7312 °2
S-0.1312 Å °-0.1246 Å °0.1041 Å °0.2677 Å °0.0687 Å °-0.1768 Å °-0.185 Å °-0.0404 Å °0.056 Å °
Refinement TLS groupSelection details: all

+
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