[English] 日本語
Yorodumi
- PDB-8v6s: Crystal structure of PcThsA in complex with Imidazole Adenine Din... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8v6s
TitleCrystal structure of PcThsA in complex with Imidazole Adenine Dinucleotide
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 / : / Thoeris protein ThsA Macro domain-containing protein
Function and homology information
Biological speciesPseudomonas corrugata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)56,3964
Polymers55,1772
Non-polymers1,2192
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-13 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.856, 87.705, 65.262
Angle α, β, γ (deg.)90.000, 97.130, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

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


Mass: 27588.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas corrugata (bacteria) / Gene: HNO91_03675 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7Y5Z1U6
#2: Chemical ChemComp-YG8 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-imidazol-1-yl-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 609.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H25N7O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14-24% w/v PEG 6000 0.2 M magnesium chloride and 0.1 M sodium acetate buffer pH 5.0

-
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: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→43.86 Å / Num. obs: 60808 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 23.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.035 / Rrim(I) all: 0.089 / Net I/σ(I): 11.3
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 1.242 / Num. unique obs: 2968 / CC1/2: 0.77 / Rpim(I) all: 0.511 / Rrim(I) all: 1.344

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→41.53 Å / SU ML: 0.2478 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.674
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2188 3069 5.06 %
Rwork0.1924 57582 -
obs0.1937 60651 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.57 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 80 318 3826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01043586
X-RAY DIFFRACTIONf_angle_d1.08864858
X-RAY DIFFRACTIONf_chiral_restr0.0628559
X-RAY DIFFRACTIONf_plane_restr0.0086609
X-RAY DIFFRACTIONf_dihedral_angle_d13.20971368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.42921670.39482544X-RAY DIFFRACTION97.48
1.63-1.650.36621340.38152582X-RAY DIFFRACTION97.73
1.65-1.680.37981190.34162626X-RAY DIFFRACTION97.93
1.68-1.710.32851470.312554X-RAY DIFFRACTION97.83
1.71-1.740.36661440.27472616X-RAY DIFFRACTION98.33
1.74-1.780.28111270.262595X-RAY DIFFRACTION98.23
1.78-1.820.24541470.23622637X-RAY DIFFRACTION98.44
1.82-1.860.23471380.21932580X-RAY DIFFRACTION98.26
1.86-1.910.26441410.22192631X-RAY DIFFRACTION98.37
1.91-1.960.23681480.22112575X-RAY DIFFRACTION98.8
1.96-2.020.2441510.23032594X-RAY DIFFRACTION98.6
2.02-2.080.25091570.23062626X-RAY DIFFRACTION98.69
2.08-2.160.19121330.18452605X-RAY DIFFRACTION98.31
2.16-2.240.20981360.17482602X-RAY DIFFRACTION98.42
2.24-2.340.21671450.17642619X-RAY DIFFRACTION98.19
2.34-2.470.1911300.18222651X-RAY DIFFRACTION98.97
2.47-2.620.19441520.17892636X-RAY DIFFRACTION99.01
2.62-2.820.23491370.19282642X-RAY DIFFRACTION99.11
2.82-3.110.2281570.19482612X-RAY DIFFRACTION99.21
3.11-3.560.22551290.1822665X-RAY DIFFRACTION99.08
3.56-4.480.18051130.14972669X-RAY DIFFRACTION98.9
4.48-41.530.15661170.16282721X-RAY DIFFRACTION98.68

+
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