+Open data
-Basic information
Entry | Database: PDB / ID: 6r6u | ||||||
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Title | Crystal structure of human cis-aconitate decarboxylase | ||||||
Components | Cis-aconitate decarboxylase | ||||||
Keywords | LYASE / 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 / cellular response to molecule of bacterial origin / negative regulation of toll-like receptor 2 signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / 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 / cellular response to molecule of bacterial origin / negative regulation of toll-like receptor 2 signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / cellular response to progesterone stimulus / negative regulation of type I interferon production / negative regulation of NF-kappaB transcription factor activity / cellular response to interferon-beta / cellular response to interleukin-1 / embryo implantation / negative regulation of innate immune response / defense response / negative regulation of inflammatory response / cellular response to type II interferon / positive regulation of reactive oxygen species metabolic process / cellular response to tumor necrosis factor / defense response to virus / cellular response to lipopolysaccharide / inflammatory response / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.705 Å | ||||||
Authors | Lukat, P. / Chen, F. / Saile, K. / Buessow, K. / Pessler, F. / Blankenfeldt, W. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r6u.cif.gz | 526.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r6u.ent.gz | 440.7 KB | Display | PDB format |
PDBx/mmJSON format | 6r6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/6r6u ftp://data.pdbj.org/pub/pdb/validation_reports/r6/6r6u | HTTPS FTP |
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-Related structure data
Related structure data | 6r6tC 2hp3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#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 / ( #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7 / Details: 0.1 M Tris-HCl pH 8.7, 1.2 M Na3-citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.45 Å2 / Biso mean: 29.1161 Å2 / Biso min: 13.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.705→60.412 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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