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- PDB-6r6u: Crystal structure of human cis-aconitate decarboxylase -

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Basic information

Entry
Database: PDB / ID: 6r6u
TitleCrystal structure of human 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 / cellular response to progesterone stimulus / negative regulation of toll-like receptor 4 signaling pathway / cellular response to molecule of bacterial origin / negative regulation of type I interferon production / : ...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 / cellular response to progesterone stimulus / negative regulation of toll-like receptor 4 signaling pathway / cellular response to molecule of bacterial origin / 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 / 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 / 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
(R,R)-2,3-BUTANEDIOL / Cis-aconitate decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.705 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)101,88012
Polymers101,3822
Non-polymers49810
Water10,989610
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-79 kcal/mol
Surface area29570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.010, 109.980, 74.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 50690.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence encoding residues 4-461 of hCAD (GenBank NM_001258406) Cys355 shows additional electron density likely due to oxidation and has thus been modeled as CSD.
Source: (gene. exp.) Homo sapiens (human) / Gene: ACOD1, IRG1 / Plasmid: pCAD29
Details (production host): modified pCOLADuet-1 with N-terminal StrepTagII and TEV protease cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus RIL / References: UniProt: A6NK06, cis-aconitate decarboxylase
#2: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7 / Details: 0.1 M Tris-HCl pH 8.7, 1.2 M Na3-citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.705→74.97 Å / Num. obs: 92409 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.024 / Rrim(I) all: 0.088 / Rsym value: 0.084 / Net I/σ(I): 22.6 / Num. measured all: 1231558
Reflection shellResolution: 1.705→1.711 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.319 / Mean I/σ(I) obs: 2 / Num. measured all: 175990 / Num. unique obs: 13315 / CC1/2: 0.85 / Rpim(I) all: 0.312 / Rrim(I) all: 1.141 / Rsym value: 1.319 / Net I/σ(I) obs: 2.5 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HP3

2hp3


Resolution: 1.705→60.412 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1624 4548 4.92 %
Rwork0.1447 87849 -
obs0.1456 92397 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.45 Å2 / Biso mean: 29.1161 Å2 / Biso min: 13.94 Å2
Refinement stepCycle: final / Resolution: 1.705→60.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7059 0 70 610 7739
Biso mean--46.35 35.69 -
Num. residues----915
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7054-1.72480.22341320.217228753007
1.7248-1.74510.27221550.212229243079
1.7451-1.76640.23471350.215728753010
1.7664-1.78870.22251710.197328863057
1.7887-1.81230.24221560.193428803036
1.8123-1.83710.21631510.179528933044
1.8371-1.86330.2151680.18228983066
1.8633-1.89120.18681430.175529003043
1.8912-1.92070.20411580.168328893047
1.9207-1.95220.22111370.167729083045
1.9522-1.98590.17741540.156728893043
1.9859-2.0220.17751750.154228933068
2.022-2.06090.18031410.151329093050
2.0609-2.10290.17141550.14428893044
2.1029-2.14870.15481520.134829423094
2.1487-2.19870.16061490.131428833032
2.1987-2.25360.1581320.129729333065
2.2536-2.31460.14531350.133429303065
2.3146-2.38270.13911410.130429573098
2.3827-2.45960.16721610.134828903051
2.4596-2.54750.16841420.133729543096
2.5475-2.64950.16451390.137429363075
2.6495-2.77010.14291350.141529633098
2.7701-2.91610.15951760.143129093085
2.9161-3.09880.1571570.14229553112
3.0988-3.33810.15691360.137529823118
3.3381-3.67390.13091740.133629323106
3.6739-4.20550.11731630.119229883151
4.2055-5.2980.14221500.121630343184
5.298-60.45020.19421750.17831533328
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)
10.74210.37320.61860.75840.15491.1231-0.07480.08240.0543-0.0510.0389-0.0976-0.11580.194800.1943-0.04050.01010.20930.03330.2179-3.362928.8451-14.4881
20.21460.0326-0.02620.471-0.00650.1095-0.009-0.01970.07340.0098-0.0424-0.0645-0.01060.0388-00.194-0.0054-0.01530.1992-0.00310.2007-4.893923.8135-7.6961
30.88240.03620.40181.48180.00010.5658-0.03760.02790.08140.0166-0.006-0.0052-0.12050.00580.00010.193-0.0048-0.0040.17220.0050.1952-12.384128.2197-13.9075
40.15310.1450.08620.17950.20010.9178-0.0198-0.04520.13510.0278-0.04270.0191-0.0953-0.092100.23740.0097-0.01460.1763-0.01540.2497-13.86729.4826-0.182
51.22790.18-0.30551.22250.39231.7746-0.0172-0.1013-0.20610.2268-0.0525-0.06340.36140.12670.00020.30020.0002-0.03840.2220.02360.2352-2.474413.336713.9999
60.3118-0.02990.10080.63410.65820.77090.0163-0.0489-0.00770.1891-0.0377-0.0905-0.09380.18300.2403-0.0051-0.05710.2090.00510.22750.714727.114813.5255
70.40540.05230.06980.10990.13460.5897-0.12690.28440.2006-0.08850.09-0.2494-0.120.4014-00.2955-0.0798-0.01480.41770.03570.382710.48535.1239-12.6577
80.90210.00670.32331.0461-0.08950.69430.03790.087-0.0717-0.0194-0.0278-0.09170.04810.0233-00.15920.0132-0.00380.1826-0.02420.1778-20.14933.8766-25.6755
91.40050.04240.50510.313-0.03380.41840.0331-0.0463-0.10110.0354-0.0077-0.02270.049-0.00540.00050.17280.00610.00290.1519-0.00830.1589-25.38125.5507-18.0218
100.7630.2291-0.58990.9536-0.24080.46570.01340.24130.08-0.14960.02620.223-0.0392-0.1556-00.25790.0122-0.0030.2588-0.00520.2578-51.121519.8984-28.6089
110.2914-0.2110.21280.2936-0.07330.35640.02140.15650.0186-0.0149-0.0023-0.0736-0.04260.157500.18740.00940.00530.23430.01020.1728-41.547819.7543-34.5775
120.9947-0.1781-0.04850.7141-0.10560.46510.03540.1507-0.0681-0.0379-0.00070.0119-0.01740.0322-00.1834-0.0018-0.01690.2155-0.02090.1621-38.42095.5772-32.9119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 77 )A4 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 104 )A78 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 227 )A105 - 227
4X-RAY DIFFRACTION4chain 'A' and (resid 228 through 296 )A228 - 296
5X-RAY DIFFRACTION5chain 'A' and (resid 297 through 385 )A297 - 385
6X-RAY DIFFRACTION6chain 'A' and (resid 386 through 426 )A386 - 426
7X-RAY DIFFRACTION7chain 'A' and (resid 427 through 461 )A427 - 461
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 177 )B5 - 177
9X-RAY DIFFRACTION9chain 'B' and (resid 178 through 295 )B178 - 295
10X-RAY DIFFRACTION10chain 'B' and (resid 296 through 326 )B296 - 326
11X-RAY DIFFRACTION11chain 'B' and (resid 327 through 359 )B327 - 359
12X-RAY DIFFRACTION12chain 'B' and (resid 360 through 461 )B360 - 461

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