[English] 日本語
Yorodumi
- PDB-8v6r: Crystal structure of EcThsA in complex with ADPR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8v6r
TitleCrystal structure of EcThsA in complex with ADPR
ComponentsThoeris protein ThsA Macro domain-containing protein
KeywordsIMMUNE SYSTEM / Antiphage immunity / nucleotide signalling
Function / homologyThoeris protein ThsA, Macro domain / Thoeris protein ThsA, Macro domain / membrane / Chem-AR6 / Thoeris protein ThsA Macro domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsShi, Y. / Masic, V. / Mosaiab, T. / Goulart, C.C. / Hartley-Tassell, L. / Sorbello, M. / Vasquez, E. / Mishra, B.P. / Holt, S. / Gu, W. ...Shi, Y. / Masic, V. / Mosaiab, T. / Goulart, C.C. / Hartley-Tassell, L. / Sorbello, M. / Vasquez, E. / Mishra, B.P. / Holt, S. / Gu, W. / Kobe, B. / Ve, T.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT200100572 Australia
CitationJournal: Sci Adv / Year: 2024
Title: Structural characterization of macro domain-containing Thoeris antiphage defense systems.
Authors: Shi, Y. / Masic, V. / Mosaiab, T. / Rajaratman, P. / Hartley-Tassell, L. / Sorbello, M. / Goulart, C.C. / Vasquez, E. / Mishra, B.P. / Holt, S. / Gu, W. / Kobe, B. / Ve, T.
History
DepositionDec 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thoeris protein ThsA Macro domain-containing protein
B: Thoeris protein ThsA Macro domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7344
Polymers55,6152
Non-polymers1,1192
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-15 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.520, 92.598, 139.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein Thoeris protein ThsA Macro domain-containing protein


Mass: 27807.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FPI65_12015 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178STJ6
#2: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14-24% w/v PEG 1000, 0.2 M lithium sulfate and 0.1 M phosphate-citrate buffer pH 3.8-4.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.14→46.66 Å / Num. obs: 29133 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 38.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.05 / Rrim(I) all: 0.111 / Net I/σ(I): 9
Reflection shellResolution: 2.14→2.2 Å / Rmerge(I) obs: 0.969 / Num. unique obs: 2281 / CC1/2: 0.667 / Rpim(I) all: 0.49 / Rrim(I) all: 1.091

-
Processing

Software
NameVersionClassification
PHENIX1.18rc3_3805refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→41.67 Å / SU ML: 0.2356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9167
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 1428 4.91 %
Rwork0.205 27632 -
obs0.2065 29060 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.66 Å2
Refinement stepCycle: LAST / Resolution: 2.14→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 72 41 3573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323606
X-RAY DIFFRACTIONf_angle_d0.58614879
X-RAY DIFFRACTIONf_chiral_restr0.0445555
X-RAY DIFFRACTIONf_plane_restr0.0028636
X-RAY DIFFRACTIONf_dihedral_angle_d15.20561360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.220.30531330.28112643X-RAY DIFFRACTION96.52
2.22-2.30.28931430.26412726X-RAY DIFFRACTION99.62
2.3-2.410.2991340.25372696X-RAY DIFFRACTION99.58
2.41-2.540.26821510.22762735X-RAY DIFFRACTION99.59
2.54-2.70.25561330.23352766X-RAY DIFFRACTION99.79
2.7-2.90.27621540.23192741X-RAY DIFFRACTION99.79
2.9-3.20.25881300.23622776X-RAY DIFFRACTION99.62
3.2-3.660.2381520.20992774X-RAY DIFFRACTION99.39
3.66-4.610.20831450.17042825X-RAY DIFFRACTION99.83
4.61-41.670.19261530.17522950X-RAY DIFFRACTION98.85
Refinement TLS params.Method: refined / Origin x: -15.0761647361 Å / Origin y: 19.3239526578 Å / Origin z: -18.4037750662 Å
111213212223313233
T0.253957836016 Å20.0388661925723 Å20.0120671603461 Å2-0.345051579548 Å2-0.00941814093385 Å2--0.327131069183 Å2
L0.684964749588 °20.811773218923 °20.392108133757 °2-4.90695492446 °22.54162137281 °2--3.19728096898 °2
S0.0329124061507 Å °-0.0577828169392 Å °-0.0886768320167 Å °0.660035538555 Å °-0.0461872289209 Å °0.185829587225 Å °0.412230582936 Å °-0.0588319007089 Å °0.00147250826309 Å °
Refinement TLS groupSelection details: all

+
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