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- PDB-12vw: R273S Human Aconitate Decarboxylase 1 mutant, apo -

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Basic information

Entry
Database: PDB / ID: 12vw
TitleR273S Human Aconitate Decarboxylase 1 mutant, apo
ComponentsCis-aconitate decarboxylase
KeywordsIMMUNE SYSTEM / immune regulatory gene 1 / oncoprotein / metabolism
Function / homology
Function and homology information


cis-aconitate decarboxylase / aconitate decarboxylase activity / tolerance induction to lipopolysaccharide / positive regulation of antimicrobial humoral response / negative regulation of toll-like receptor 2 signaling pathway / cellular response to progesterone stimulus / negative regulation of toll-like receptor 4 signaling pathway / cellular response to molecule of bacterial origin / cellular response to cocaine / negative regulation of type I interferon production ...cis-aconitate decarboxylase / aconitate decarboxylase activity / tolerance induction to lipopolysaccharide / positive regulation of antimicrobial humoral response / negative regulation of toll-like receptor 2 signaling pathway / cellular response to progesterone stimulus / negative regulation of toll-like receptor 4 signaling pathway / cellular response to molecule of bacterial origin / cellular response to cocaine / negative regulation of type I interferon production / cellular response to interleukin-1 / cellular response to interferon-beta / embryo implantation / negative regulation of innate immune response / cellular response to tumor necrosis factor / defense response / cellular response to type II interferon / negative regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / cellular response to lipopolysaccharide / defense response to virus / inflammatory response / protein homodimerization activity / mitochondrion
Similarity search - Function
MmgE/PrpD / MmgE/PrpD superfamily / MmgE/PrpD superfamily, domain 1 / MmgE/PrpD superfamily, domain 2 / MmgE/PrpD, N-terminal / MmgE/PrpD, C-terminal / MmgE/PrpD N-terminal domain / MmgE/PrpD C-terminal domain
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Cis-aconitate decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsRunge, B. / Monteiro, D.C.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J Struct Biol X / Year: 2026
Title: Robust structural, kinetic and biophysical characterization of wild-type human ACOD1, selected mutants and their interaction with citraconate
Authors: Runge, B. / Oktay, H. / Fucci, I.J. / Merten, E.M. / Tarasov, S.G. / Fan, L. / Monteiro, D.C.
History
DepositionApr 20, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cis-aconitate decarboxylase
B: Cis-aconitate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3835
Polymers101,1772
Non-polymers2053
Water17,529973
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-27 kcal/mol
Surface area30530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.871, 110.186, 75.733
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cis-aconitate decarboxylase / CAD / Aconitate decarboxylase / Aconitate decarboxylase 1 / Cis-aconitic acid decarboxylase / ...CAD / Aconitate decarboxylase / Aconitate decarboxylase 1 / Cis-aconitic acid decarboxylase / Immune-responsive gene 1 protein


Mass: 50588.703 Da / Num. of mol.: 2 / Mutation: Y318A
Source method: isolated from a genetically manipulated source
Details: truncated construct without disordered regions (1-3 and 462-481)
Source: (gene. exp.) Homo sapiens (human) / Gene: ACOD1, IRG1 / Production host: Escherichia coli (E. coli) / References: UniProt: A6NK06, cis-aconitate decarboxylase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 973 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 100 mM Tris pH 8.8, 35% PEG 4000, 200 mM CaOAc, 200 nL drop, 2:1 protein:reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.46→44.55 Å / Num. obs: 129053 / % possible obs: 96.2 % / Redundancy: 8.7 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.05 / Rrim(I) all: 0.154 / Net I/σ(I): 8.4
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.48 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6453 / CC1/2: 0.621 / Rpim(I) all: 0.537 / Rrim(I) all: 1.65 / % possible all: 64.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.105)refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→44.55 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.039 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1844 6449 4.997 %RANDOM
Rwork0.1539 122604 --
all0.155 ---
obs-129053 87.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.333 Å2
Baniso -1Baniso -2Baniso -3
1-0.109 Å2-0 Å20 Å2
2--0.222 Å2-0 Å2
3----0.331 Å2
Refinement stepCycle: LAST / Resolution: 1.46→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7084 0 12 973 8069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127379
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167010
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.80710059
X-RAY DIFFRACTIONr_angle_other_deg0.6051.74116165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645940
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.984538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67101198
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.10510300
X-RAY DIFFRACTIONr_chiral_restr0.0890.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021651
X-RAY DIFFRACTIONr_nbd_refined0.2280.21727
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.26672
X-RAY DIFFRACTIONr_nbtor_refined0.1850.23686
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2726
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0150.22
X-RAY DIFFRACTIONr_metal_ion_refined0.3790.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3170.240
X-RAY DIFFRACTIONr_nbd_other0.2250.2126
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2930.2114
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0620.21
X-RAY DIFFRACTIONr_mcbond_it1.2061.0123728
X-RAY DIFFRACTIONr_mcbond_other1.2061.0113727
X-RAY DIFFRACTIONr_mcangle_it1.9311.8114678
X-RAY DIFFRACTIONr_mcangle_other1.9311.8124679
X-RAY DIFFRACTIONr_scbond_it2.0461.2663651
X-RAY DIFFRACTIONr_scbond_other2.0421.2653650
X-RAY DIFFRACTIONr_scangle_it3.1932.2075381
X-RAY DIFFRACTIONr_scangle_other3.1922.2065379
X-RAY DIFFRACTIONr_lrange_it5.65915.4598929
X-RAY DIFFRACTIONr_lrange_other5.47612.2258591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.4970.376310.299709X-RAY DIFFRACTION6.8354
1.497-1.5380.2852480.2654553X-RAY DIFFRACTION45.4425
1.538-1.5830.2643930.2487505X-RAY DIFFRACTION76.8064
1.583-1.6310.2524600.2278734X-RAY DIFFRACTION91.6467
1.631-1.6850.2184820.2089107X-RAY DIFFRACTION99.2137
1.685-1.7440.2284520.1938935X-RAY DIFFRACTION100
1.744-1.810.2154500.1758656X-RAY DIFFRACTION100
1.81-1.8830.2114290.1698279X-RAY DIFFRACTION100
1.883-1.9670.2024370.1597941X-RAY DIFFRACTION100
1.967-2.0630.193980.157628X-RAY DIFFRACTION100
2.063-2.1740.1783750.1457299X-RAY DIFFRACTION100
2.174-2.3060.173910.1346868X-RAY DIFFRACTION100
2.306-2.4640.1653270.1316475X-RAY DIFFRACTION100
2.464-2.6610.1623350.1296024X-RAY DIFFRACTION100
2.661-2.9140.1982920.1375618X-RAY DIFFRACTION100
2.914-3.2560.1672570.1415089X-RAY DIFFRACTION100
3.256-3.7570.1792750.1434461X-RAY DIFFRACTION100
3.757-4.5930.1541770.1283873X-RAY DIFFRACTION100
4.593-6.4610.1581530.1583050X-RAY DIFFRACTION100
6.461-44.550.163870.1661800X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.20260.21140.28230.54350.03820.44710.0108-0.0531-0.02540.0053-0.00060.00370.0108-0.0009-0.01020.01730.00550.00710.0050.00540.01929.52267.026926.3055
20.43720.00350.32040.468-0.00391.1466-0.01910.01190.0548-0.017-0.01380.0194-0.0297-0.05960.03290.02760.0005-0.00940.01080.0110.0785.832725.82113.1403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp4 - 501
2X-RAY DIFFRACTION2ALLBp4 - 501

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