[English] 日本語
Yorodumi
- PDB-8k0v: Crystal structure of theophylline DNA aptamer bound to 3-methylxa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k0v
TitleCrystal structure of theophylline DNA aptamer bound to 3-methylxanthine
ComponentsDNA (29-MER)
KeywordsDNA / Aptamer / Theophylline / 3-methylxanthine
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsHuang, Y. / Lin, X. / Huang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: From Theophylline to Adenine or preQ 1 : Repurposing a DNA Aptamer Revealed by Crystal Structure Analysis.
Authors: Lin, X. / Huang, Y. / Huang, J. / Yuan, H. / Luo, Y. / Lu, Z. / Ao, Y. / Huang, J. / Chen, S.B. / Miao, Z. / Huang, L.
History
DepositionJul 10, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 18, 2025Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1776
Polymers8,9191
Non-polymers2585
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-10 kcal/mol
Surface area4830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.292, 49.292, 50.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-208-

HOH

-
Components

#1: DNA chain DNA (29-MER)


Mass: 8918.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-I7U / 3-methyl-7~{H}-purine-2,6-dione / 3-Methylxanthine / 1076-22-8


Mass: 166.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 53 / 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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Calcium chloride dihydrate 24% v/v Polyethylene glycol 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Mar 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.67→50.96 Å / Num. obs: 8671 / % possible obs: 100 % / Redundancy: 17.2 % / Biso Wilson estimate: 19.25 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.5
Reflection shellResolution: 1.67→1.71 Å / Num. unique obs: 640 / CC1/2: 0.954

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→42.69 Å / SU ML: 0.2559 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.0781
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 469 5.52 %
Rwork0.2412 8034 -
obs0.2415 8503 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.99 Å2
Refinement stepCycle: LAST / Resolution: 1.67→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 591 16 53 660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014674
X-RAY DIFFRACTIONf_angle_d1.51211038
X-RAY DIFFRACTIONf_chiral_restr0.0831115
X-RAY DIFFRACTIONf_plane_restr0.011630
X-RAY DIFFRACTIONf_dihedral_angle_d32.6284286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.910.46991130.43972581X-RAY DIFFRACTION95.23
1.91-2.410.3271800.28192663X-RAY DIFFRACTION99.82
2.41-42.690.19691760.19442790X-RAY DIFFRACTION99.7
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7512813531-0.490872530273-1.811779202124.62557411845-1.706344109253.954952351820.149639705206-0.603366627872-0.623631555372-0.5042278820430.477533629514-0.0768259274331-0.116327798479-0.272656112879-0.5266553096060.410567235064-0.08757449097970.0687358217230.440146590520.08403773806590.31032056680516.710807743-6.07242343437-10.6409186303
27.003511402881.633263369980.3945127011482.664527264350.8548689016024.745655534070.285049016766-0.257068806392-0.02748218579560.33680313389-0.1456146145430.033868694419-0.0116999558305-0.00418052398987-0.1542724824120.202848019237-0.03137188204890.01077787313160.1820841265240.0265452962320.18534906333315.718589448-13.83702684877.69009579045
34.560927304361.90559071372-1.109941442537.17430294286-4.005460856835.666514945960.2478585675540.182203758510.3659455217680.03628006259290.3403948650561.06748989988-0.49047007489-0.218051161748-0.5311973506940.2294969401790.02136884475420.0238934500280.2682819275080.01263796256260.20406256085711.4898371129-8.58757424477-5.30867292392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )AA1 - 5
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 20 )AA6 - 20
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 29 )AA21 - 29

+
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