[English] 日本語
Yorodumi
- PDB-8d28: Crystal structure of theophylline aptamer in complex with theophylline -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8d28
TitleCrystal structure of theophylline aptamer in complex with theophylline
ComponentsRNA (33-MER)
KeywordsRNA / aptamer / theophylline
Function / homologyTHEOPHYLLINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsMenichelli, E. / Spraggon, G.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Discovery of small molecules that target a tertiary-structured RNA.
Authors: Menichelli, E. / Lam, B.J. / Wang, Y. / Wang, V.S. / Shaffer, J. / Tjhung, K.F. / Bursulaya, B. / Nguyen, T.N. / Vo, T. / Alper, P.B. / McAllister, C.S. / Jones, D.H. / Spraggon, G. / ...Authors: Menichelli, E. / Lam, B.J. / Wang, Y. / Wang, V.S. / Shaffer, J. / Tjhung, K.F. / Bursulaya, B. / Nguyen, T.N. / Vo, T. / Alper, P.B. / McAllister, C.S. / Jones, D.H. / Spraggon, G. / Michellys, P.Y. / Joslin, J. / Joyce, G.F. / Rogers, J.
History
DepositionMay 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: RNA (33-MER)
A: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,84913
Polymers21,2752
Non-polymers57411
Water6,521362
1
B: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9618
Polymers10,6371
Non-polymers3237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8885
Polymers10,6371
Non-polymers2504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.074, 29.561, 80.397
Angle α, β, γ (deg.)95.730, 90.090, 109.580
Int Tables number1
Space group name H-MP1

-
Components

#1: RNA chain RNA (33-MER)


Mass: 10637.426 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-TEP / THEOPHYLLINE


Mass: 180.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium cacodylate, PEG 8000, 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.42→39.97 Å / Num. obs: 35223 / % possible obs: 93.76 % / Redundancy: 2.1 % / CC1/2: 0.999 / Net I/σ(I): 15.19
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 2.1 % / Num. unique obs: 3451 / CC1/2: 0.886 / % possible all: 91.54

-
Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O15

1o15


Resolution: 1.42→39.97 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 1748 4.97 %
Rwork0.1739 33456 -
obs0.1755 35204 93.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.51 Å2 / Biso mean: 25.2168 Å2 / Biso min: 9.51 Å2
Refinement stepCycle: final / Resolution: 1.42→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1408 51 362 1821
Biso mean--17.77 30.96 -
Num. residues----66
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.42-1.460.25991470.2392727287491
1.46-1.510.23421620.22132686284892
1.51-1.560.21251410.20582808294993
1.56-1.630.2421530.19682788294194
1.63-1.70.22181340.19352766290094
1.7-1.790.22581800.20132775295593
1.79-1.90.2161360.18682827296394
1.9-2.050.20171330.18472792292594
2.05-2.250.17681570.17532805296294
2.25-2.580.25051500.18722831298195
2.58-3.250.20411470.17432783293094
3.25-39.970.18041080.14052868297695

+
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