[English] 日本語
Yorodumi
- PDB-8h4o: Crystal Structure of nucleotide-free Irgb6_T95D mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8h4o
TitleCrystal Structure of nucleotide-free Irgb6_T95D mutant
ComponentsT-cell-specific guanine nucleotide triphosphate-binding protein 2
KeywordsIMMUNE SYSTEM / Toxoplasma gondii / PV / IRG / GTPase / HYDROLASE
Function / homology
Function and homology information


defense response to protozoan / cellular response to interferon-beta / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response / innate immune response / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus
Similarity search - Function
Immunity-related GTPases-like / IRG-type guanine nucleotide-binding (G) domain / Interferon-inducible GTPase (IIGP) / IRG-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
T-cell-specific guanine nucleotide triphosphate-binding protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSaijo-Hamano, Y. / Okuma, H. / Sakai, N. / Kato, T. / Imasaki, T. / Nitta, R.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21gm0810013 Japan
Japan Society for the Promotion of Science (JSPS)21K06988 Japan
Japan Society for the Promotion of Science (JSPS)21H05254 Japan
Japan Society for the Promotion of Science (JSPS)21K19352 Japan
Japan Society for the Promotion of Science (JSPS)22H02795 Japan
Japan Science and TechnologyJPMJMS2024 Japan
CitationJournal: To Be Published
Title: Structural basis of Irgb6 inactivation by Toxoplasma gondii through the phosphorylation of switch I
Authors: Okuma, H. / Saijo-Hamano, Y. / Sherif, A.A. / Hashizaki, E. / Sakai, N. / Kato, K. / Imasaki, T. / Nitta, E. / Sasai, M. / Kosako, H. / Standley, D.M. / Yamamoto, M. / Nitta, R.
History
DepositionOct 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-cell-specific guanine nucleotide triphosphate-binding protein 2
B: T-cell-specific guanine nucleotide triphosphate-binding protein 2


Theoretical massNumber of molelcules
Total (without water)94,6892
Polymers94,6892
Non-polymers00
Water1,74797
1
A: T-cell-specific guanine nucleotide triphosphate-binding protein 2


Theoretical massNumber of molelcules
Total (without water)47,3451
Polymers47,3451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T-cell-specific guanine nucleotide triphosphate-binding protein 2


Theoretical massNumber of molelcules
Total (without water)47,3451
Polymers47,3451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.532, 80.613, 147.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein T-cell-specific guanine nucleotide triphosphate-binding protein 2 / Interferon-gamma-inducible GTPase Ifggb6 protein / T-cell-specific guanine nucleotide triphosphate- ...Interferon-gamma-inducible GTPase Ifggb6 protein / T-cell-specific guanine nucleotide triphosphate-binding protein


Mass: 47344.703 Da / Num. of mol.: 2 / Mutation: T95D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tgtp2, Ifggb6, Irgb6, Mg21, Tgtp / Production host: Escherichia coli (E. coli)
References: UniProt: Q3T9E4, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Sodium malonate, PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 54351 / % possible obs: 99.4 % / Redundancy: 6.95 % / CC1/2: 0.998 / Net I/σ(I): 10.25
Reflection shellResolution: 2.05→2.17 Å / Num. unique obs: 16439 / CC1/2: 0.508

-
Processing

Software
NameVersionClassification
PHENIX1.20_4459: ???refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VEX, 7VES

7vex

7ves


Resolution: 2.05→40.55 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2828 1999 3.68 %
Rwork0.2256 --
obs0.2277 54351 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6392 0 0 97 6489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.886
X-RAY DIFFRACTIONf_dihedral_angle_d5.303842
X-RAY DIFFRACTIONf_chiral_restr0.05978
X-RAY DIFFRACTIONf_plane_restr0.011125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.3711340.31673511X-RAY DIFFRACTION95
2.1-2.150.32781420.28213684X-RAY DIFFRACTION99
2.15-2.220.32651410.27323697X-RAY DIFFRACTION99
2.22-2.290.3521400.26283694X-RAY DIFFRACTION100
2.29-2.370.30621420.25593718X-RAY DIFFRACTION99
2.37-2.460.36481410.25333704X-RAY DIFFRACTION100
2.46-2.580.31861430.25123732X-RAY DIFFRACTION100
2.58-2.710.30421420.25493704X-RAY DIFFRACTION100
2.71-2.880.34271440.26463757X-RAY DIFFRACTION100
2.88-3.10.30051430.2493777X-RAY DIFFRACTION100
3.1-3.420.27771440.24933754X-RAY DIFFRACTION100
3.42-3.910.29551450.22543791X-RAY DIFFRACTION100
3.91-4.930.25731460.18973832X-RAY DIFFRACTION100
4.93-40.550.23681520.19553997X-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