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- PDB-12vq: H103A Human Aconitate Decarboxylase 1 mutant, apo -

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Basic information

Entry
Database: PDB / ID: 12vq
TitleH103A 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 / defense response to virus / cellular response to lipopolysaccharide / 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: 1.42 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.F.
History
DepositionApr 20, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2026Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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)101,6199
Polymers101,1842
Non-polymers4357
Water18,7361040
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-49 kcal/mol
Surface area30490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.824, 110.018, 75.844
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-501-

PEG

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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: 50591.750 Da / Num. of mol.: 2 / Mutation: H103A
Source method: isolated from a genetically manipulated source
Details: truncated construct, missing 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

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Non-polymers , 6 types, 1047 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1040 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
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: 0.92021 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92021 Å / Relative weight: 1
ReflectionResolution: 1.42→34.5 Å / Num. obs: 129811 / % possible obs: 95.4 % / Redundancy: 13.9 % / Biso Wilson estimate: 16.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.049 / Rrim(I) all: 0.189 / Net I/σ(I): 10.1
Reflection shellResolution: 1.42→1.54 Å / Redundancy: 14.2 % / Rmerge(I) obs: 2.43 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6491 / CC1/2: 0.598 / Rpim(I) all: 0.696 / Rrim(I) all: 2.62 / % possible all: 51.9

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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: 1.42→34.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.797 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1813 6630 5.107 %RANDOM
Rwork0.1503 123181 --
all0.152 ---
obs-129811 80.408 %-
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: 16.789 Å2
Baniso -1Baniso -2Baniso -3
1--0.067 Å2-0 Å20 Å2
2--0.092 Å20 Å2
3----0.025 Å2
Refinement stepCycle: LAST / Resolution: 1.42→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7088 0 26 1040 8154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127505
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167179
X-RAY DIFFRACTIONr_angle_refined_deg1.731.8110251
X-RAY DIFFRACTIONr_angle_other_deg0.6031.74216558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.316542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84101238
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.59410311
X-RAY DIFFRACTIONr_chiral_restr0.0880.21167
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021695
X-RAY DIFFRACTIONr_nbd_refined0.2340.21753
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.26847
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23697
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23949
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2784
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1240.25
X-RAY DIFFRACTIONr_metal_ion_refined0.1620.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2640.238
X-RAY DIFFRACTIONr_nbd_other0.2380.2162
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.2108
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0430.21
X-RAY DIFFRACTIONr_mcbond_it1.0670.8533753
X-RAY DIFFRACTIONr_mcbond_other1.0650.8523752
X-RAY DIFFRACTIONr_mcangle_it1.7351.5294713
X-RAY DIFFRACTIONr_mcangle_other1.7341.5294714
X-RAY DIFFRACTIONr_scbond_it1.6741.0753752
X-RAY DIFFRACTIONr_scbond_other1.6721.0733751
X-RAY DIFFRACTIONr_scangle_it2.6591.8745513
X-RAY DIFFRACTIONr_scangle_other2.6591.8725511
X-RAY DIFFRACTIONr_lrange_it5.35813.0739130
X-RAY DIFFRACTIONr_lrange_other5.14210.7478761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.4540.21950.25284X-RAY DIFFRACTION0.7537
1.454-1.4940.238300.256590X-RAY DIFFRACTION5.388
1.494-1.5370.2851850.2573895X-RAY DIFFRACTION36.3831
1.537-1.5850.2744470.2538712X-RAY DIFFRACTION84.1743
1.585-1.6370.2555210.2299870X-RAY DIFFRACTION98.6519
1.637-1.6940.2365140.2069728X-RAY DIFFRACTION99.922
1.694-1.7580.2185090.1849362X-RAY DIFFRACTION100
1.758-1.8290.1884910.1699027X-RAY DIFFRACTION100
1.829-1.910.1924480.1598683X-RAY DIFFRACTION100
1.91-2.0030.1864340.1498314X-RAY DIFFRACTION100
2.003-2.1110.1754470.1387895X-RAY DIFFRACTION100
2.111-2.2390.1694120.1347468X-RAY DIFFRACTION100
2.239-2.3930.1683610.1297063X-RAY DIFFRACTION100
2.393-2.5830.1713520.136579X-RAY DIFFRACTION100
2.583-2.8280.1693620.1356062X-RAY DIFFRACTION100
2.828-3.1590.1763270.1345497X-RAY DIFFRACTION100
3.159-3.6430.1592740.1334889X-RAY DIFFRACTION100
3.643-4.450.1452350.1224182X-RAY DIFFRACTION100
4.45-6.2410.1861610.1383314X-RAY DIFFRACTION100
6.241-34.50.1671150.1631967X-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)
11.1710.21290.27230.46360.04830.37190.0159-0.0475-0.02450.0142-0.0059-0.00590.00380.0054-0.00990.0210.00850.00730.00690.00420.003529.5057.013626.3399
20.4507-0.01170.28680.4402-0.00681.0992-0.01280.02120.0588-0.0278-0.01260.0286-0.0164-0.04570.02540.03130.0026-0.00610.00750.01210.05085.747125.88193.1375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA4 - 503
2X-RAY DIFFRACTION2ALLB4 - 504

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