[English] 日本語
Yorodumi
- PDB-8kbe: Structure of CbTad1 complexed with 1',3'-cADPR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8kbe
TitleStructure of CbTad1 complexed with 1',3'-cADPR
ComponentsThoeris anti-defense 1
KeywordsVIRAL PROTEIN
Function / homologynucleotide binding / Chem-OJC / Thoeris anti-defense 1
Function and homology information
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsXiao, Y. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2024
Title: Single phage proteins sequester signals from TIR and cGAS-like enzymes.
Authors: Li, D. / Xiao, Y. / Fedorova, I. / Xiong, W. / Wang, Y. / Liu, X. / Huiting, E. / Ren, J. / Gao, Z. / Zhao, X. / Cao, X. / Zhang, Y. / Bondy-Denomy, J. / Feng, Y.
History
DepositionAug 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thoeris anti-defense 1
B: Thoeris anti-defense 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8084
Polymers31,7252
Non-polymers1,0832
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-38 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.090, 101.090, 101.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

-
Components

#1: Protein Thoeris anti-defense 1


Mass: 15862.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: tad1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW58
#2: Chemical ChemComp-OJC / (2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione


Mass: 541.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N5O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 3.2 M Ammonium sulfate, 0.1 M Citrate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.16→35.74 Å / Num. obs: 18785 / % possible obs: 100 % / Redundancy: 35.1 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.012 / Rrim(I) all: 0.071 / Χ2: 0.95 / Net I/σ(I): 31.3 / Num. measured all: 660157
Reflection shellResolution: 2.16→2.22 Å / % possible obs: 100 % / Redundancy: 17.8 % / Rmerge(I) obs: 1.232 / Num. measured all: 24972 / Num. unique obs: 1399 / CC1/2: 0.791 / Rpim(I) all: 0.293 / Rrim(I) all: 1.268 / Χ2: 0.83 / Net I/σ(I) obs: 2.3

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7uaw

7uaw


Resolution: 2.16→31.97 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 941 5.02 %
Rwork0.2051 --
obs0.2071 18756 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→31.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 70 45 2174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062168
X-RAY DIFFRACTIONf_angle_d1.2752921
X-RAY DIFFRACTIONf_dihedral_angle_d15.428422
X-RAY DIFFRACTIONf_chiral_restr0.062315
X-RAY DIFFRACTIONf_plane_restr0.005373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.270.32121300.26962516X-RAY DIFFRACTION100
2.27-2.420.28531560.23062475X-RAY DIFFRACTION100
2.42-2.60.32021440.27832537X-RAY DIFFRACTION100
2.6-2.860.30161300.27262517X-RAY DIFFRACTION100
2.86-3.280.28881250.23842539X-RAY DIFFRACTION100
3.28-4.130.21591270.19662574X-RAY DIFFRACTION100
4.13-31.970.22771290.16772657X-RAY DIFFRACTION100

+
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