+Open data
-Basic information
Entry | Database: PDB / ID: 6q6q | ||||||
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Title | Human aldehyde oxidase SNP G1269R | ||||||
Components | Aldehyde oxidase | ||||||
Keywords | OXIDOREDUCTASE / Single-nucleotide Polymorphism / Moco-free form | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor / aldehyde oxidase / aldehyde oxidase activity / Vitamin B6 activation to pyridoxal phosphate / molybdopterin cofactor binding / xenobiotic metabolic process / FAD binding / 2 iron, 2 sulfur cluster binding / lipid metabolic process / NAD binding ...Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor / aldehyde oxidase / aldehyde oxidase activity / Vitamin B6 activation to pyridoxal phosphate / molybdopterin cofactor binding / xenobiotic metabolic process / FAD binding / 2 iron, 2 sulfur cluster binding / lipid metabolic process / NAD binding / flavin adenine dinucleotide binding / iron ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.10003770671 Å | ||||||
Authors | Mota, C. / Coelho, C. / Santos-Silva, T. / Romao, M.J. | ||||||
Funding support | Portugal, 1items
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Citation | Journal: Febs Open Bio / Year: 2019 Title: Human aldehyde oxidase (hAOX1): structure determination of the Moco-free form of the natural variant G1269R and biophysical studies of single nucleotide polymorphisms. Authors: Mota, C. / Esmaeeli, M. / Coelho, C. / Santos-Silva, T. / Wolff, M. / Foti, A. / Leimkuhler, S. / Romao, M.J. #1: Journal: Febs Open Bio / Year: 2019 Title: Human aldehyde oxidase (hAOX1): structure determination of the Moco‐free form of the natural variant G1269R and biophysical studies of single nucleotide polymorphisms Authors: Mota, C. / Esmaeeli, M. / Coelho, C. / Santos-Silva, T. / Wolff, M. / Foti, A. / Leimkuhler, S. / Romao, M.J. #2: Journal: Nat. Chem. Biol. / Year: 2015 Title: Structural insights into xenobiotic and inhibitor binding to human aldehyde oxidase Authors: Coelho, C. / Foti, A. / Hartmann, T. / Santos-Silva, T. / Leimkuhler, S. / Romao, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q6q.cif.gz | 289.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q6q.ent.gz | 208.8 KB | Display | PDB format |
PDBx/mmJSON format | 6q6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/6q6q ftp://data.pdbj.org/pub/pdb/validation_reports/q6/6q6q | HTTPS FTP |
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-Related structure data
Related structure data | 4uhxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 148196.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AOX1, AO / Production host: Escherichia coli (E. coli) References: UniProt: Q06278, aldehyde oxidase, Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Chemical | ChemComp-MLI / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG3350, Sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→49.4 Å / Num. obs: 50950 / % possible obs: 99.9 % / Redundancy: 8.4 % / Biso Wilson estimate: 84.2337235282 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.04 / Rrim(I) all: 0.117 / Rsym value: 0.11 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 3.1→3.29 Å / Rmerge(I) obs: 0.921 / Rpim(I) all: 0.331 / Rrim(I) all: 0.981 / Rsym value: 0.921 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UHX Resolution: 3.10003770671→46.8640062404 Å / SU ML: 0.384293005148 / Cross valid method: FREE R-VALUE / σ(F): 0.204487145437 / Phase error: 23.729061676
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.6965461748 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.10003770671→46.8640062404 Å
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Refine LS restraints |
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LS refinement shell |
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