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- PDB-8jqy: Crystal Structure of nucleotide-free mIRGB10 -

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Basic information

Entry
Database: PDB / ID: 8jqy
TitleCrystal Structure of nucleotide-free mIRGB10
ComponentsImmunity-related GTPase family member b10
KeywordsIMMUNE SYSTEM / GTP hydrolase
Function / homology
Function and homology information


autophagosome assembly / cellular response to interferon-beta / innate immune response / GTPase activity / endoplasmic reticulum membrane / GTP binding
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
Immunity-related GTPase family member b10
Similarity search - Component
Biological speciesMus musculus molossinus (Japanese wild mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.68 Å
AuthorsHa, H.J. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Front Immunol / Year: 2023
Title: Structural basis of IRGB10 oligomerization by GTP hydrolysis.
Authors: Ha, H.J. / Kim, J.H. / Lee, G.H. / Kim, S. / Park, H.H.
History
DepositionJun 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunity-related GTPase family member b10


Theoretical massNumber of molelcules
Total (without water)47,1201
Polymers47,1201
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20800 Å2
Unit cell
Length a, b, c (Å)190.240, 190.240, 38.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Immunity-related GTPase family member b10


Mass: 47119.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus molossinus (Japanese wild mouse)
Gene: Irgb10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: U5NFV2

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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: 4.31 Å3/Da / Density % sol: 71.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.0 M ammonium sulfate, 0.2 M lithium sulfate, and 0.1 M Tris-HCl (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 3.68→29.61 Å / Num. obs: 8893 / % possible obs: 99.66 % / Redundancy: 20.7 % / Biso Wilson estimate: 138.93 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.54
Reflection shellResolution: 3.681→3.812 Å / Num. unique obs: 891 / CC1/2: 0.671 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.68→29.61 Å / SU ML: 0.5468 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.3371
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2719 445 5 %
Rwork0.2494 8448 -
obs0.2506 8893 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 155.45 Å2
Refinement stepCycle: LAST / Resolution: 3.68→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 0 0 3032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313087
X-RAY DIFFRACTIONf_angle_d0.57284147
X-RAY DIFFRACTIONf_chiral_restr0.0391467
X-RAY DIFFRACTIONf_plane_restr0.0042520
X-RAY DIFFRACTIONf_dihedral_angle_d15.8627395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.68-4.210.35241470.30422799X-RAY DIFFRACTION99.97
4.21-5.30.27181460.26492781X-RAY DIFFRACTION99.97
5.3-29.610.25111520.22652868X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 66.3207665273 Å / Origin y: -60.7203405647 Å / Origin z: -16.2434791357 Å
111213212223313233
T0.973005193152 Å2-0.132083006104 Å20.0552964811254 Å2-1.10567549051 Å2-0.166691527998 Å2--0.746623402245 Å2
L6.94417862078 °24.30082760241 °21.20595507003 °2-3.82504868282 °20.908918757118 °2--1.52598697179 °2
S-0.0387887486796 Å °-0.0665297104066 Å °0.0534613638682 Å °-0.0748343371049 Å °0.0367011361808 Å °-0.389646994231 Å °0.0771965240444 Å °-0.365030171179 Å °0.0522445935203 Å °
Refinement TLS groupSelection details: all

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