[English] 日本語
Yorodumi
- PDB-1et4: CRYSTAL STRUCTURE OF A VITAMIN B12 BINDING RNA APTAMER WITH LIGAN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1et4
TitleCRYSTAL STRUCTURE OF A VITAMIN B12 BINDING RNA APTAMER WITH LIGAND AT 2.3 A
ComponentsRNA APTAMER, 35-MER
KeywordsRNA / B12 BINDING RNA / VITAMIN B12 / COBALAMIN
Function / homologyCYANOCOBALAMIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsSussman, D. / Wilson, C.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: A water channel in the core of the vitamin B(12) RNA aptamer.
Authors: Sussman, D. / Wilson, C.
History
DepositionApr 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 2.0Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_validate_chiral / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA APTAMER, 35-MER
B: RNA APTAMER, 35-MER
C: RNA APTAMER, 35-MER
D: RNA APTAMER, 35-MER
E: RNA APTAMER, 35-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,18610
Polymers56,4045
Non-polymers6,7825
Water13,061725
1
A: RNA APTAMER, 35-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6372
Polymers11,2811
Non-polymers1,3561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA APTAMER, 35-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6372
Polymers11,2811
Non-polymers1,3561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA APTAMER, 35-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6372
Polymers11,2811
Non-polymers1,3561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA APTAMER, 35-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6372
Polymers11,2811
Non-polymers1,3561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RNA APTAMER, 35-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6372
Polymers11,2811
Non-polymers1,3561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.27, 98.08, 217.97
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222

-
Components

#1: RNA chain
RNA APTAMER, 35-MER


Mass: 11280.819 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: COMPLEXED WITH CYANO COBALAMIN
#2: Chemical
ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C63H89CoN14O14P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / 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: 4.32 Å3/Da / Density % sol: 71.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 6.9 M LICL, 8.0 % ISOPROPANOL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1ISOPROPANOL11
2LICL11
3ISOPROPANOL12
4LICL12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16.5-6.9 M1reservoirLiCl
26-8 %isopropanol1reservoir
315 %isopropanol1drop
42.5-5 mM1dropMgCl2

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.6
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. all: 39042 / Num. obs: 39042 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.095
Reflection
*PLUS
% possible obs: 89.2 %
Reflection shell
*PLUS
% possible obs: 57.7 % / Rmerge(I) obs: 0.311

-
Processing

Software
NameClassification
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→10 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1914 5.3 %RANDOM
Rwork0.199 ---
obs0.199 35761 --
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3755 465 725 4945
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 220 Å / % reflection Rfree: 5.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4

+
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