[English] 日本語
Yorodumi
- PDB-9iwf: crystal structure of P. beijingensis xanthine-II riboswitch in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9iwf
Titlecrystal structure of P. beijingensis xanthine-II riboswitch in complex with xanthine
ComponentsP. beijingensis xanthine-II riboswitch (70-MER)
KeywordsRNA / riboswitch / xanthine
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / XANTHINE / : / RNA / RNA (> 10)
Function and homology information
Biological speciesPaenibacillus beijingensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsXu, X.C. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci China Life Sci / Year: 2025
Title: Structure-based principles underlying ligand recognition of xanthine-II riboswitch.
Authors: Xu, X. / He, M. / Tai, X. / Ren, Q. / Shen, X. / Li, C. / Ren, A.
History
DepositionJul 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P. beijingensis xanthine-II riboswitch (70-MER)
B: P. beijingensis xanthine-II riboswitch (70-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,84121
Polymers44,1262
Non-polymers1,71519
Water1,982110
1
A: P. beijingensis xanthine-II riboswitch (70-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,93311
Polymers22,0631
Non-polymers87010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P. beijingensis xanthine-II riboswitch (70-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,90910
Polymers22,0631
Non-polymers8459
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.585, 115.752, 126.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: RNA chain P. beijingensis xanthine-II riboswitch (70-MER)


Mass: 22063.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Paenibacillus beijingensis (bacteria) / References: GenBank: 779742186
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Magnesium chloride, 0.04 M Sodium cacodylate pH 5.5, 40% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.002 M Hexammine cobalt(III) chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.06→85.48 Å / Num. obs: 24728 / % possible obs: 97.2 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Χ2: 0.92 / Net I/σ(I): 19.5 / Num. measured all: 307642
Reflection shellResolution: 2.06→2.17 Å / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 1.198 / Num. measured all: 46330 / Num. unique obs: 3588 / CC1/2: 0.793 / Rpim(I) all: 0.344 / Rrim(I) all: 1.247 / Χ2: 0.83 / Net I/σ(I) obs: 2.4

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→30.56 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1999 8.11 %
Rwork0.2187 --
obs0.2215 24648 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→30.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2986 37 110 3133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053354
X-RAY DIFFRACTIONf_angle_d1.1315216
X-RAY DIFFRACTIONf_dihedral_angle_d16.3581698
X-RAY DIFFRACTIONf_chiral_restr0.051698
X-RAY DIFFRACTIONf_plane_restr0.007144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.110.37641390.3321576X-RAY DIFFRACTION100
2.11-2.160.35611450.3061642X-RAY DIFFRACTION100
2.16-2.230.38771460.29791656X-RAY DIFFRACTION100
2.23-2.30.34311100.2881248X-RAY DIFFRACTION78
2.3-2.380.34161460.29171657X-RAY DIFFRACTION100
2.38-2.480.30231440.2941633X-RAY DIFFRACTION100
2.48-2.590.311480.30651661X-RAY DIFFRACTION100
2.59-2.730.41511430.31361629X-RAY DIFFRACTION100
2.73-2.90.38291470.30631680X-RAY DIFFRACTION100
2.9-3.120.30051460.26161641X-RAY DIFFRACTION100
3.12-3.430.2371480.21011677X-RAY DIFFRACTION100
3.43-3.930.24781240.18831413X-RAY DIFFRACTION83
3.93-4.950.18711520.1631710X-RAY DIFFRACTION100
4.95-30.560.17991610.1691826X-RAY DIFFRACTION99

+
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