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- PDB-8jqz: Crystal Structure of GppNHp-bound mIRGB10 -

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Basic information

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


defense response to other organism / cellular response to interferon-beta / GTPase activity / endoplasmic reticulum membrane / GTP binding
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Immunity-related GTPase family member b10
Similarity search - Component
Biological speciesMus musculus molossinus (Japanese wild mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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
B: Immunity-related GTPase family member b10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2844
Polymers94,2392
Non-polymers1,0442
Water00
1
A: Immunity-related GTPase family member b10
hetero molecules

B: Immunity-related GTPase family member b10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2844
Polymers94,2392
Non-polymers1,0442
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area2960 Å2
ΔGint-11 kcal/mol
Surface area38250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.640, 62.440, 119.230
Angle α, β, γ (deg.)90.000, 99.562, 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: 47119.605 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: U5NFV2
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 2,000 monomethyl ether (MME), 0.2 M trimethylamine n-oxide, 0.1 M Tris-HCl (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→29.43 Å / Num. obs: 17524 / % possible obs: 99.44 % / Redundancy: 6.6 % / Biso Wilson estimate: 84.19 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.86
Reflection shellResolution: 3.05→3.159 Å / Redundancy: 6.8 % / Num. unique obs: 1743 / CC1/2: 0.866 / % possible all: 99.43

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→29.43 Å / SU ML: 0.5123 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.6238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.265 876 5.01 %
Rwork0.2319 16618 -
obs0.2337 17494 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.03 Å2
Refinement stepCycle: LAST / Resolution: 3.05→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6073 0 64 0 6137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00296261
X-RAY DIFFRACTIONf_angle_d0.91538428
X-RAY DIFFRACTIONf_chiral_restr0.0388933
X-RAY DIFFRACTIONf_plane_restr0.00421048
X-RAY DIFFRACTIONf_dihedral_angle_d8.2324796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.240.38431440.34112726X-RAY DIFFRACTION99.58
3.24-3.490.35571450.28752752X-RAY DIFFRACTION99.55
3.49-3.840.31161460.25622754X-RAY DIFFRACTION99.66
3.84-4.40.22851440.21842766X-RAY DIFFRACTION99.59
4.4-5.530.25471460.21522770X-RAY DIFFRACTION99.66
5.53-29.430.23191510.20612850X-RAY DIFFRACTION99.37
Refinement TLS params.Method: refined / Origin x: 36.8027082296 Å / Origin y: -21.5252278279 Å / Origin z: 28.8807013495 Å
111213212223313233
T0.738993731942 Å2-0.0923586877182 Å2-0.0298418082722 Å2-0.545417469924 Å20.0202652762172 Å2--0.543744565663 Å2
L0.919260166642 °2-0.558199099495 °20.18896662166 °2-0.881653141287 °2-0.0280150726807 °2--1.13850112336 °2
S0.0984238656611 Å °0.204703476041 Å °0.0439619821559 Å °-0.293188377049 Å °-0.114391310704 Å °0.0420296209117 Å °-0.19555674186 Å °-0.0290402733249 Å °0.0212500971716 Å °
Refinement TLS groupSelection details: all

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