[English] 日本語
Yorodumi
- PDB-8g0k: Bacteroides multispecies type VI secretion system Ntox15 domain e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8g0k
TitleBacteroides multispecies type VI secretion system Ntox15 domain effector and immunity Tde1/Tdi1
Components
  • DUF1851 domain-containing protein
  • Ntox15 domain-containing protein
KeywordsTOXIN / type VI secretion system / Bacteroides / effector / immunity
Biological speciesBacteroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBosch, D.E. / Mougous, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K08 AI159619 United States
CitationJournal: Mbio / Year: 2023
Title: Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales.
Authors: Bosch, D.E. / Abbasian, R. / Parajuli, B. / Peterson, S.B. / Mougous, J.D.
History
DepositionJan 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ntox15 domain-containing protein
B: DUF1851 domain-containing protein
C: Ntox15 domain-containing protein
D: DUF1851 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)91,4404
Polymers91,4404
Non-polymers00
Water6,305350
1
A: Ntox15 domain-containing protein
B: DUF1851 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)45,7202
Polymers45,7202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-23 kcal/mol
Surface area15580 Å2
MethodPISA
2
C: Ntox15 domain-containing protein
D: DUF1851 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)45,7202
Polymers45,7202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-19 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.770, 112.272, 149.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Ntox15 domain-containing protein


Mass: 22863.316 Da / Num. of mol.: 2 / Mutation: H279A, D282A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides (bacteria) / Production host: Escherichia coli BL21 (bacteria)
#2: Protein DUF1851 domain-containing protein


Mass: 22856.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides (bacteria) / Production host: Escherichia coli BL21 (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG 3350, 200 mM lithium sulfate, 100 mM Bis-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 46798 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 34.02 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.6
Reflection shellResolution: 2.2→2.22 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2 / Num. unique obs: 1159 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.2refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.79 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 1990 4.26 %
Rwork0.2074 --
obs0.2095 46670 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5257 0 0 350 5607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135359
X-RAY DIFFRACTIONf_angle_d1.1687215
X-RAY DIFFRACTIONf_dihedral_angle_d6.174689
X-RAY DIFFRACTIONf_chiral_restr0.06787
X-RAY DIFFRACTIONf_plane_restr0.007915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.3641240.24712898X-RAY DIFFRACTION91
2.25-2.310.29591460.23593183X-RAY DIFFRACTION100
2.31-2.380.27151340.22243207X-RAY DIFFRACTION100
2.38-2.460.30581440.21963167X-RAY DIFFRACTION100
2.46-2.550.26141450.21653196X-RAY DIFFRACTION100
2.55-2.650.28241410.21783164X-RAY DIFFRACTION100
2.65-2.770.30451470.21283193X-RAY DIFFRACTION100
2.77-2.920.28131410.21213217X-RAY DIFFRACTION100
2.92-3.10.23131420.21863185X-RAY DIFFRACTION100
3.1-3.340.2721410.21423219X-RAY DIFFRACTION100
3.34-3.670.25791430.19153220X-RAY DIFFRACTION100
3.67-4.20.23331450.18263210X-RAY DIFFRACTION99
4.21-5.290.22341430.18023248X-RAY DIFFRACTION99
5.29-34.790.24991540.22893373X-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