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- PDB-7c3k: Crystal Structure of mIRGB10 -

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Basic information

Entry
Database: PDB / ID: 7c3k
TitleCrystal Structure of mIRGB10
ComponentsImmunity-related GTPase family member b10
KeywordsIMMUNE SYSTEM / mIRGB
Function / homology
Function and homology information


cellular response to interferon-beta / defense 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
GUANOSINE-5'-DIPHOSPHATE / Immunity-related GTPase family member b10
Similarity search - Component
Biological speciesMus musculus molossinus (Japanese wild mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHa, H.J. / Jeong, J.H. / Kim, Y.G. / Park, H.H.
CitationJournal: Commun Biol / Year: 2021
Title: Molecular basis of IRGB10 oligomerization and membrane association for pathogen membrane disruption.
Authors: Ha, H.J. / Chun, H.L. / Lee, S.Y. / Jeong, J.H. / Kim, Y.G. / Park, H.H.
History
DepositionMay 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunity-related GTPase family member b10
B: Immunity-related GTPase family member b10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2974
Polymers93,4102
Non-polymers8862
Water1,27971
1
A: Immunity-related GTPase family member b10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1482
Polymers46,7051
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19820 Å2
MethodPISA
2
B: Immunity-related GTPase family member b10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1482
Polymers46,7051
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-7 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.510, 63.190, 117.920
Angle α, β, γ (deg.)90.000, 98.700, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Immunity-related GTPase family member b10


Mass: 46705.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus molossinus (Japanese wild mouse)
Gene: Irgb10 / Production host: Escherichia coli (E. coli) / References: UniProt: U5NFV2
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 8,000, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9779 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 14, 2019 / Details: Vertical focusing toroidal, rhodium coated
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.6→29.14 Å / Num. obs: 28239 / % possible obs: 99.82 % / Redundancy: 7 % / Biso Wilson estimate: 44.99 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07632 / Rpim(I) all: 0.03095 / Rrim(I) all: 0.08245 / Net I/σ(I): 17.57
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.4301 / Mean I/σ(I) obs: 3.95 / Num. unique obs: 2784 / CC1/2: 0.96 / CC star: 0.99 / Rpim(I) all: 0.1699 / Rrim(I) all: 0.4628 / % possible all: 99.82

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tpA

1tpa


Resolution: 2.6→29.14 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2718 --
Rwork0.2133 --
obs-28215 99.82 %
Displacement parametersBiso mean: 54.32 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 56 71 6343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00286398
X-RAY DIFFRACTIONf_angle_d0.58368616
X-RAY DIFFRACTIONf_chiral_restr0.0421958
X-RAY DIFFRACTIONf_plane_restr0.00421078
X-RAY DIFFRACTIONf_dihedral_angle_d16.65753902

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