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- PDB-7br9: Crystal structure of mus musculus IRG1 -

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Basic information

Entry
Database: PDB / ID: 7br9
TitleCrystal structure of mus musculus IRG1
ComponentsCis-aconitate decarboxylase
KeywordsSTRUCTURAL PROTEIN / IRG1 / cis-Aconitate decarboxylase / Immune-responsive gene 1 protein
Function / homology
Function and homology information


cis-aconitate decarboxylase / positive regulation of antimicrobial humoral response / aconitate decarboxylase activity / tolerance induction to lipopolysaccharide / cellular response to molecule of bacterial origin / negative regulation of toll-like receptor 2 signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / cellular response to progesterone stimulus / negative regulation of type I interferon production / negative regulation of NF-kappaB transcription factor activity ...cis-aconitate decarboxylase / positive regulation of antimicrobial humoral response / aconitate decarboxylase activity / tolerance induction to lipopolysaccharide / cellular response to molecule of bacterial origin / negative regulation of toll-like receptor 2 signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / cellular response to progesterone stimulus / negative regulation of type I interferon production / negative regulation of NF-kappaB transcription factor activity / cellular response to interferon-beta / cellular response to interleukin-1 / embryo implantation / negative regulation of innate immune response / response to bacterium / defense response / negative regulation of inflammatory response / cellular response to type II interferon / positive regulation of reactive oxygen species metabolic process / cellular response to tumor necrosis factor / defense response to virus / cellular response to lipopolysaccharide / response to lipopolysaccharide / inflammatory response / protein homodimerization activity / mitochondrion
Similarity search - Function
MmgE/PrpD, N-terminal / MmgE/PrpD, C-terminal / MmgE/PrpD / MmgE/PrpD superfamily / MmgE/PrpD superfamily, domain 1 / MmgE/PrpD superfamily, domain 2 / MmgE/PrpD N-terminal domain / MmgE/PrpD C-terminal domain
Similarity search - Domain/homology
Cis-aconitate decarboxylase / Cis-aconitate decarboxylase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsPark, H.H. / Chun, H.L.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Plos One / Year: 2020
Title: The crystal structure of mouse IRG1 suggests that cis-aconitate decarboxylase has an open and closed conformation.
Authors: Chun, H.L. / Lee, S.Y. / Kim, K.H. / Lee, C.S. / Oh, T.J. / Park, H.H.
History
DepositionMar 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: Cis-aconitate decarboxylase
B: Cis-aconitate decarboxylase


Theoretical massNumber of molelcules
Total (without water)107,6352
Polymers107,6352
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-21 kcal/mol
Surface area30000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.493, 55.610, 90.956
Angle α, β, γ (deg.)90.00, 107.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cis-aconitate decarboxylase


Mass: 53817.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Acod1, Irg1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0R4J027, UniProt: P54987*PLUS

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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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.17M Lithium sulfate monohydrate 0.085M Tris-HCl pH 8.5 25.5% (w/v) PEG 4000 15% glycerol

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Data collection

DiffractionMean temperature: 125 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: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.29→29.45 Å / Num. obs: 13873 / % possible obs: 98.8 % / Redundancy: 5.9 % / Rsym value: 0.232 / Net I/σ(I): 5.71
Reflection shellResolution: 3.3→3.36 Å / Num. unique obs: 678 / Rsym value: 0.543

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R6T

6r6t


Resolution: 3.3→29.45 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2568 1385 9.98 %
Rwork0.2168 --
obs0.2208 13873 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6986 0 0 0 6986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047161
X-RAY DIFFRACTIONf_angle_d0.8079727
X-RAY DIFFRACTIONf_dihedral_angle_d7.621955
X-RAY DIFFRACTIONf_chiral_restr0.0491102
X-RAY DIFFRACTIONf_plane_restr0.0061251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.410.30061230.26851113X-RAY DIFFRACTION89
3.41-3.540.27071370.25681226X-RAY DIFFRACTION97
3.55-3.710.28471360.24561232X-RAY DIFFRACTION98
3.71-3.90.32181370.23961231X-RAY DIFFRACTION99
3.9-4.140.26371400.22181269X-RAY DIFFRACTION99
4.15-4.460.21991390.19331243X-RAY DIFFRACTION99
4.46-4.910.24421410.19241283X-RAY DIFFRACTION100
4.91-5.620.2521430.19961280X-RAY DIFFRACTION100
5.62-7.060.23411430.2121289X-RAY DIFFRACTION100
7.06-29.450.21011460.18271322X-RAY DIFFRACTION100

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