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- PDB-7vex: Crystal Structure of GTP-bound Irgb6 -

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Basic information

Entry
Database: PDB / ID: 7vex
TitleCrystal Structure of GTP-bound Irgb6
ComponentsT-cell-specific guanine nucleotide triphosphate-binding protein 2
KeywordsHYDROLASE / Irgb6 / IRGs / immunity-related GTPase / (IFN)-inducible GTPase / p47 GTPase / tgtp / dynamin superfamily / IMMUNE SYSTEM
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
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: 1.51 Å
AuthorsSaijo-Hamano, Y. / Sakai, N. / Nitta, R.
Funding support Japan, 12items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20fk0108137 Japan
Japan Agency for Medical Research and Development (AMED)JP20wm0325010 Japan
Japan Agency for Medical Research and Development (AMED)JP20jm0210067 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101108 Japan
Japan Agency for Medical Research and Development (AMED)JP20gm0810013 Japan
Japan Society for the Promotion of Science (JSPS)21K06988 Japan
Japan Society for the Promotion of Science (JSPS)20B304 Japan
Japan Society for the Promotion of Science (JSPS)19H04809 Japan
Japan Society for the Promotion of Science (JSPS)19H00970 Japan
Japan Society for the Promotion of Science (JSPS)19H03396 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101070 Japan
Japan Society for the Promotion of Science (JSPS)JPMJMS2024 Japan
CitationJournal: Life Sci Alliance / Year: 2022
Title: Structural basis of membrane recognition of Toxoplasma gondii vacuole by Irgb6.
Authors: Saijo-Hamano, Y. / Sherif, A.A. / Pradipta, A. / Sasai, M. / Sakai, N. / Sakihama, Y. / Yamamoto, M. / Standley, D.M. / Nitta, R.
History
DepositionSep 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)47,8542
Polymers47,3311
Non-polymers5231
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-2 kcal/mol
Surface area20290 Å2
Unit cell
Length a, b, c (Å)69.618, 75.743, 80.620
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: 47330.719 Da / Num. of mol.: 1
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 / Guanosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium Citrate, 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: Jun 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→43.29 Å / Num. obs: 129901 / % possible obs: 99.9 % / Redundancy: 6.99 % / CC1/2: 0.999 / Net I/σ(I): 15.07
Reflection shellResolution: 1.51→1.6 Å / Num. unique obs: 20925 / CC1/2: 0.524

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TQD, 1TPZ, 1TQ2

1tqd

1tpz

1tq2


Resolution: 1.51→43.29 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.194 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19687 1997 2.9 %RANDOM
Rwork0.14686 ---
obs0.14831 65855 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.227 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å2-0 Å2-0 Å2
2---0.8 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.51→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 32 303 3639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133436
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173222
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.6454661
X-RAY DIFFRACTIONr_angle_other_deg1.4681.587461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6735414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14323.964169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0115602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3221511
X-RAY DIFFRACTIONr_chiral_restr0.090.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023825
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02761
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.6833.141650
X-RAY DIFFRACTIONr_mcbond_other5.6563.1371649
X-RAY DIFFRACTIONr_mcangle_it6.994.7062060
X-RAY DIFFRACTIONr_mcangle_other6.9894.7092061
X-RAY DIFFRACTIONr_scbond_it6.7273.6581786
X-RAY DIFFRACTIONr_scbond_other6.7273.6581784
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.055.2672600
X-RAY DIFFRACTIONr_long_range_B_refined8.11537.8563955
X-RAY DIFFRACTIONr_long_range_B_other8.03337.4633878
X-RAY DIFFRACTIONr_rigid_bond_restr4.46836658
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.51→1.55 Å
RfactorNum. reflection% reflection
Rfree0.458 142 -
Rwork0.477 4817 -
obs--99.48 %

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