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- PDB-8h4m: Crystal Structure of GTP-bound Irgb6_T95D mutant -

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Basic information

Entry
Database: PDB / ID: 8h4m
TitleCrystal Structure of GTP-bound 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / innate immune response / GTPase activity / GTP binding / endoplasmic reticulum / Golgi apparatus / membrane
Similarity search - Function
Immunity-related GTPases-like / : / Interferon-inducible GTPase (IIGP) / IRG-type guanine nucleotide-binding (G) domain / IRG-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / T-cell-specific guanine nucleotide triphosphate-binding protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,8682
Polymers47,3451
Non-polymers5231
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-2 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.122, 75.750, 80.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 1 / 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: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium sulfate, polyethylene glycol 3350

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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: 1.67→50 Å / Num. obs: 49012 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 11.55
Reflection shellResolution: 1.68→1.78 Å / Num. unique obs: 14962 / CC1/2: 0.475

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Processing

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

7vex


Resolution: 1.68→37.88 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 2000 4.08 %
Rwork0.2059 --
obs0.2069 49012 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 32 167 3464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.921
X-RAY DIFFRACTIONf_dihedral_angle_d16.149451
X-RAY DIFFRACTIONf_chiral_restr0.057504
X-RAY DIFFRACTIONf_plane_restr0.007582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.42151300.38443266X-RAY DIFFRACTION98
1.72-1.760.33531470.32733316X-RAY DIFFRACTION100
1.76-1.820.32151420.27743301X-RAY DIFFRACTION100
1.82-1.870.29111300.24353320X-RAY DIFFRACTION100
1.87-1.940.26311500.23463346X-RAY DIFFRACTION100
1.94-2.020.23911480.22893293X-RAY DIFFRACTION100
2.02-2.110.26861310.22873346X-RAY DIFFRACTION100
2.11-2.220.23691540.19863367X-RAY DIFFRACTION100
2.22-2.360.23481320.20563347X-RAY DIFFRACTION100
2.36-2.540.2361480.20873335X-RAY DIFFRACTION100
2.54-2.80.27051430.21113381X-RAY DIFFRACTION100
2.8-3.210.22441440.21013401X-RAY DIFFRACTION100
3.21-4.040.21191490.18633414X-RAY DIFFRACTION100
4.04-50.19521520.1843579X-RAY DIFFRACTION100

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