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- PDB-12ux: WT Human Aconitate Decarboxylase 1, apo -

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Basic information

Entry
Database: PDB / ID: 12ux
TitleWT Human Aconitate Decarboxylase 1, 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cis-aconitate decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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)101,6376
Polymers101,3182
Non-polymers3194
Water18,0871004
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-43 kcal/mol
Surface area30850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.678, 110.021, 75.755
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1099-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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: 50658.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: truncated construct with disordered regions deleted (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

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Non-polymers , 5 types, 1008 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1004 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris pH 8.0, 25% 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: Feb 10, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.32→33.78 Å / Num. obs: 146042 / % possible obs: 94.1 % / Redundancy: 13.7 % / Biso Wilson estimate: 11.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.057 / Rrim(I) all: 0.22 / Net I/σ(I): 9.8
Reflection shellResolution: 1.32→1.49 Å / Redundancy: 11.6 % / Rmerge(I) obs: 2.5 / Mean I/σ(I) obs: 1 / Num. unique obs: 7306 / CC1/2: 0.331 / Rpim(I) all: 0.789 / Rrim(I) all: 2.742 / % possible all: 55.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→33.78 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.161 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1925 7369 5.046 %
Rwork0.1582 138673 -
all0.16 --
obs-146042 74.009 %
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: 17.596 Å2
Baniso -1Baniso -2Baniso -3
1-0.025 Å20 Å20 Å2
2---0.232 Å20 Å2
3---0.207 Å2
Refinement stepCycle: LAST / Resolution: 1.32→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7109 0 19 1004 8132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0127499
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167159
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.80910232
X-RAY DIFFRACTIONr_angle_other_deg0.61.74116498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.39543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.631101224
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.97710311
X-RAY DIFFRACTIONr_chiral_restr0.0870.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021705
X-RAY DIFFRACTIONr_nbd_refined0.2310.21794
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.26968
X-RAY DIFFRACTIONr_nbtor_refined0.1870.23741
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2831
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1520.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.227
X-RAY DIFFRACTIONr_nbd_other0.2390.2124
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.263
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.7570.21
X-RAY DIFFRACTIONr_mcbond_it1.2541.0053755
X-RAY DIFFRACTIONr_mcbond_other1.2531.0053755
X-RAY DIFFRACTIONr_mcangle_it2.0071.84716
X-RAY DIFFRACTIONr_mcangle_other2.0081.84717
X-RAY DIFFRACTIONr_scbond_it2.2141.2983744
X-RAY DIFFRACTIONr_scbond_other2.2131.2993745
X-RAY DIFFRACTIONr_scangle_it3.542.2415503
X-RAY DIFFRACTIONr_scangle_other3.542.2425504
X-RAY DIFFRACTIONr_lrange_it6.22413.9239196
X-RAY DIFFRACTIONr_lrange_other5.98212.2778840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.3580.18810.55118X-RAY DIFFRACTION0.1319
1.358-1.3950.60360.47851X-RAY DIFFRACTION0.4049
1.395-1.4360.447600.3561075X-RAY DIFFRACTION8.2642
1.436-1.480.3512900.325709X-RAY DIFFRACTION45.1494
1.48-1.5280.2965120.2879873X-RAY DIFFRACTION80.2178
1.528-1.5820.2726220.25711511X-RAY DIFFRACTION97.204
1.582-1.6410.2385750.22911499X-RAY DIFFRACTION99.9255
1.641-1.7080.2225720.20811045X-RAY DIFFRACTION100
1.708-1.7840.2275790.19210620X-RAY DIFFRACTION100
1.784-1.8710.2135540.17810126X-RAY DIFFRACTION100
1.871-1.9710.25300.1629662X-RAY DIFFRACTION100
1.971-2.0910.1844800.1459153X-RAY DIFFRACTION100
2.091-2.2340.1714580.1328628X-RAY DIFFRACTION100
2.234-2.4130.1654360.1248029X-RAY DIFFRACTION99.9882
2.413-2.6410.1773850.137468X-RAY DIFFRACTION100
2.641-2.9510.1873580.1436727X-RAY DIFFRACTION99.7326
2.951-3.4030.1643100.1365981X-RAY DIFFRACTION99.6042
3.403-4.1570.1742560.1255130X-RAY DIFFRACTION99.9258
4.157-5.8360.1592440.1223997X-RAY DIFFRACTION100
5.836-33.780.1631410.1452371X-RAY DIFFRACTION99.564
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)
10.71650.1106-0.14760.2972-0.06760.25260.0027-0.03130.00520.0012-0.00340.0065-0.0014-0.00620.00070.01240.0035-0.00290.025-0.00590.001921.4105-6.9572-11.6982
20.3026-0.0185-0.1840.36190.06160.6534-0.0280.0228-0.0656-0.028-0.0115-0.01620.02940.02340.03960.0329-0.00050.01960.0284-0.00890.040844.9534-25.7825-34.8279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA3 - 461
2X-RAY DIFFRACTION2ALLB4 - 461

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