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- PDB-6r6t: Crystal structure of mouse cis-aconitate decarboxylase -

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Basic information

Entry
Database: PDB / ID: 6r6t
TitleCrystal structure of mouse cis-aconitate decarboxylase
ComponentsCis-aconitate decarboxylase
KeywordsLYASE / Immunity / Inflammatory response / Innate immunity / Antimicrobial / Decarboxylase / cis-Aconitate / Itaconate
Function / homology
Function and homology information


cis-aconitate decarboxylase / positive regulation of antimicrobial humoral response / aconitate decarboxylase activity / tolerance induction to lipopolysaccharide / negative regulation of toll-like receptor 2 signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / cellular response to molecule of bacterial origin / 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 / negative regulation of toll-like receptor 2 signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / cellular response to molecule of bacterial origin / cellular response to progesterone stimulus / negative regulation of type I interferon production / negative regulation of NF-kappaB transcription factor activity / cellular response to interleukin-1 / cellular response to interferon-beta / embryo implantation / negative regulation of innate immune response / response to bacterium / defense response / cellular response to type II interferon / negative regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / defense response to virus / 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
Aconitate decarboxylase 1 / Cis-aconitate decarboxylase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.535 Å
AuthorsLukat, P. / Chen, F. / Saile, K. / Buessow, K. / Pessler, F. / Blankenfeldt, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Crystal structure ofcis-aconitate decarboxylase reveals the impact of naturally occurring human mutations on itaconate synthesis.
Authors: Chen, F. / Lukat, P. / Iqbal, A.A. / Saile, K. / Kaever, V. / van den Heuvel, J. / Blankenfeldt, W. / Bussow, K. / Pessler, F.
History
DepositionMar 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _software.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


Theoretical massNumber of molelcules
Total (without water)115,7432
Polymers115,7432
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-24 kcal/mol
Surface area30760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.074, 174.074, 71.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cis-aconitate decarboxylase


Mass: 57871.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Acod1, Irg1 / Plasmid: pCAD09 / Details (production host): transient gene expression / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0R4J027, UniProt: P54987*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Condition 29 (60% tacsimate pH 7.0) of the INDEX sparse matrix screen (Hampton Research).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.535→123.089 Å / Num. obs: 36057 / % possible obs: 97.3 % / Redundancy: 14.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.033 / Rrim(I) all: 0.127 / Rsym value: 0.122 / Net I/σ(I): 18 / Num. measured all: 527814
Reflection shellResolution: 2.535→2.578 Å / Redundancy: 15.3 % / Rmerge(I) obs: 1.583 / Mean I/σ(I) obs: 2 / Num. measured all: 71632 / Num. unique obs: 4757 / CC1/2: 0.655 / Rpim(I) all: 0.37 / Rrim(I) all: 1.444 / Rsym value: 1.583 / Net I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
autoPROC(Version 1.0.5)data collection
XDS(VERSION Nov 1data reduction
autoPROC(Version 1.0.5)data scaling
pointlessdata scaling
Aimlessdata scaling
BALBESphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HP3

2hp3


Resolution: 2.535→77.848 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 1864 5.17 %
Rwork0.2107 34186 -
obs0.2125 36050 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.41 Å2 / Biso mean: 68.543 Å2 / Biso min: 33.98 Å2
Refinement stepCycle: final / Resolution: 2.535→77.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6946 0 0 47 6993
Biso mean---49.63 -
Num. residues----901
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5345-2.60310.31991520.319526302782100
2.6031-2.67970.3207930.31411880197399
2.6797-2.76620.33521260.299225432669100
2.7662-2.8650.32581240.300926652789100
2.865-2.97980.32831380.282226802818100
2.9798-3.11540.27991320.267226832815100
3.1154-3.27960.2931610.250926502811100
3.2796-3.48510.25231680.234326712839100
3.4851-3.75420.24081560.208726832839100
3.7542-4.1320.22321440.184127142858100
4.132-4.72980.22231480.166327252873100
4.7298-5.95870.2261580.179427602918100
5.9587-77.8850.20791640.175129023066100
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)
11.129-0.00870.65051.5061-1.11061.3009-0.0003-0.1311-0.05880.616-0.0421-0.28320.3175-0.00110.00010.62-0.0881-0.03390.44190.11560.5178136.216277.810242.1468
20.11440.0552-0.09950.22740.26540.5774-0.3695-0.1362-0.4695-0.02440.1732-1.26270.08871.0280.00280.5359-0.0088-0.03920.7750.17560.9427147.014176.431631.9092
30.5684-0.4839-0.89573.1515-1.08072.6117-0.0088-0.17390.00930.6284-0.04140.0747-0.09470.1964-0.00010.6202-0.0291-0.04230.46390.09160.4389131.794679.494741.7183
40.7210.2559-0.16092.7544-0.42531.66350.0568-0.0263-0.03290.4561-0.0814-0.0228-0.1962-0.069-00.5196-0.0310.02090.44960.08970.4162127.903385.057638.6143
50.3769-0.54380.02030.765-0.09060.5503-0.18590.1877-0.21790.16130.01310.57490.325-0.0485-0.00010.57730.0493-0.01820.44980.03920.6706118.891544.717939.0127
60.77840.2069-0.42480.70850.61481.0343-0.02040.72260.1074-0.7808-0.05880.2326-0.3433-0.06710.00010.61650.0714-0.03310.51750.17170.6531121.435756.587229.8138
71.88310.68050.37560.8788-0.71621.22160.20340.5983-0.2296-0.0238-0.24650.22130.2393-0.05590.00010.56750.11460.06410.62820.06360.5879120.19653.773433.025
80.7157-0.1393-0.34392.2346-0.20561.63940.23160.037-0.36710.5221-0.22380.1210.0476-0.0368-0.00010.69310.05660.04250.49330.09110.6095126.021855.196744.8022
90.60760.40240.43670.52170.26590.4277-0.1373-0.1840.05430.4101-0.0841-0.48430.46690.3137-0.00570.71290.0367-0.2840.70060.21380.744148.989770.593349.6016
100.7707-0.19290.02473.33730.42311.8696-0.0820.00180.0334-0.5465-0.0699-0.1641-0.1190.05340.00010.5572-0.0490.05760.47540.10540.4697135.959593.874312.8911
110.60781.10640.62333.487-0.47482.6522-0.057-0.0666-0.0816-0.71010.0129-0.2386-0.0046-0.10290.00010.6739-0.01110.04860.3720.0720.4488131.473988.06689.9669
121.14360.1844-0.22552.019-0.61862.2746-0.17750.0701-0.123-0.24640.16510.17710.1484-0.118200.4423-0.02540.03680.36650.05320.4889127.324382.245117.6961
131.1268-0.1253-0.20811.1821-0.61210.70360.0665-0.08540.1768-0.5246-0.37240.64360.0854-0.22430.00020.5963-0.0429-0.13450.4748-0.03680.5321120.4529115.007311.3315
140.73760.07480.33830.13580.20930.79270.2354-1.0245-0.09880.5181-0.5910.19330.6243-0.20250.00010.729-0.16530.07010.8632-0.01970.7196121.9183114.054224.3966
151.4611-0.388-0.81131.5152-0.45611.38020.2772-0.55410.35970.0237-0.20060.355-0.3827-0.06770.00020.6022-0.0556-0.03770.6413-0.08960.571120.2753116.78721.3126
161.50770.21680.89832.41980.31771.01930.09530.27380.0213-0.8374-0.24060.5525-0.1925-0.18650.00330.7154-0.166-0.06860.42940.08770.5795124.1666115.57819.0849
170.13380.06640.05730.34970.13570.34820.00520.4552-0.0375-0.6450.0707-0.5688-0.0419-0.00580.00571.0456-0.11190.36610.71410.09410.6859146.067999.79361.0327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 59 )A3 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 88 )A60 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 175 )A89 - 175
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 276 )A176 - 276
5X-RAY DIFFRACTION5chain 'A' and (resid 277 through 312 )A277 - 312
6X-RAY DIFFRACTION6chain 'A' and (resid 313 through 344 )A313 - 344
7X-RAY DIFFRACTION7chain 'A' and (resid 345 through 385 )A345 - 385
8X-RAY DIFFRACTION8chain 'A' and (resid 386 through 431 )A386 - 431
9X-RAY DIFFRACTION9chain 'A' and (resid 432 through 460 )A432 - 460
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 107 )B1 - 107
11X-RAY DIFFRACTION11chain 'B' and (resid 108 through 175 )B108 - 175
12X-RAY DIFFRACTION12chain 'B' and (resid 176 through 255 )B176 - 255
13X-RAY DIFFRACTION13chain 'B' and (resid 256 through 312 )B256 - 312
14X-RAY DIFFRACTION14chain 'B' and (resid 313 through 344 )B313 - 344
15X-RAY DIFFRACTION15chain 'B' and (resid 345 through 385 )B345 - 385
16X-RAY DIFFRACTION16chain 'B' and (resid 386 through 431 )B386 - 431
17X-RAY DIFFRACTION17chain 'B' and (resid 432 through 459 )B432 - 459

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