[English] 日本語
Yorodumi
- PDB-9ec4: Structure of the Bacillus subtilis yjdF riboswitch aptamer domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ec4
TitleStructure of the Bacillus subtilis yjdF riboswitch aptamer domain in complex with chelerythrine
ComponentsRNA (81-MER)
KeywordsRNA / riboswitch / chelerythrine / aptamer
Function / homology: / Chem-CTI / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.853 Å
AuthorsBatey, R.T. / Spradlin, S.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM152029 United States
CitationJournal: To Be Published
Title: Structure of the Bacillus subtilis yjdF riboswitch aptamer domain in complex with lumichrome
Authors: Batey, R.T. / Spradlin, S.F.
History
DepositionNov 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
M: RNA (81-MER)
A: RNA (81-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,07026
Polymers52,4252
Non-polymers1,64424
Water1,58588
1
M: RNA (81-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,98613
Polymers26,2131
Non-polymers77312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: RNA (81-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,08413
Polymers26,2131
Non-polymers87112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.654, 69.270, 82.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11M-110-

MG

-
Components

-
RNA chain , 1 types, 2 molecules MA

#1: RNA chain RNA (81-MER)


Mass: 26212.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 5 types, 112 molecules

#2: Chemical ChemComp-CTI / 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium / chelerythrine


Mass: 348.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ba
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 5% MPD, 3 mM spermine, 40 mM Na-cacodylate pH 7.0, 20 mM KCl, 5 mM BaCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 18, 2022
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. obs: 14791 / % possible obs: 98.7 % / Redundancy: 4.1 % / Rpim(I) all: 0.045 / Rsym value: 0.085 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.85-2.953.50.53514120.9230.980.3130.6240.99397.4
2.95-3.073.60.25114480.9870.9970.1430.2911.07797.7
3.07-3.2140.12414400.9950.9990.0660.1411.20898.2
3.21-3.3840.11414500.9950.9990.060.1291.3298.6
3.38-3.594.20.10714900.9960.9990.0560.1211.41699.5
3.59-3.864.40.09714710.9940.9990.0510.111.7699.5
3.86-4.254.40.08914830.9960.9990.0470.1011.67499.2
4.25-4.854.40.08415050.9930.9980.0440.0951.79999.2
4.85-6.094.40.06415030.9950.9990.0330.0731.97699.3
6.09-203.90.04515890.9960.9990.0260.0522.78798.3

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.853→19.794 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 1447 9.99 %
Rwork0.2286 --
obs0.2322 14483 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.853→19.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3476 74 88 3638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023951
X-RAY DIFFRACTIONf_angle_d0.616154
X-RAY DIFFRACTIONf_dihedral_angle_d12.461928
X-RAY DIFFRACTIONf_chiral_restr0.021808
X-RAY DIFFRACTIONf_plane_restr0.002164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.853-2.95460.4371300.38191193X-RAY DIFFRACTION88
2.9546-3.07250.48161420.35921256X-RAY DIFFRACTION95
3.0725-3.21180.29031360.25251272X-RAY DIFFRACTION95
3.2118-3.38030.27381440.25141269X-RAY DIFFRACTION96
3.3803-3.5910.26711490.25021322X-RAY DIFFRACTION98
3.591-3.86630.26071430.21741325X-RAY DIFFRACTION98
3.8663-4.25190.23841460.22151308X-RAY DIFFRACTION97
4.2519-4.85920.2461470.20451322X-RAY DIFFRACTION97
4.8592-6.09230.21171510.20191347X-RAY DIFFRACTION98
6.0923-19.7940.25191590.20351422X-RAY DIFFRACTION98

+
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