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Yorodumi- PDB-7q86: Crystal structure of human peroxisomal acyl-Co-A oxidase 1a, FAD-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q86 | |||||||||
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Title | Crystal structure of human peroxisomal acyl-Co-A oxidase 1a, FAD-bound-form | |||||||||
Components | Isoform 2 of Peroxisomal acyl-coenzyme A oxidase 1 | |||||||||
Keywords | OXIDOREDUCTASE / acyl-Co-A oxidase / peroxisomal enzyme | |||||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | |||||||||
Authors | Sonani, R.R. / Blat, A. / Dubin, G. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2022 Title: Crystal structures of apo- and FAD-bound human peroxisomal acyl-CoA oxidase provide mechanistic basis explaining clinical observations. Authors: Sonani, R.R. / Blat, A. / Dubin, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q86.cif.gz | 498.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q86.ent.gz | 404.7 KB | Display | PDB format |
PDBx/mmJSON format | 7q86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q86_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7q86_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7q86_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 7q86_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/7q86 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/7q86 | HTTPS FTP |
-Related structure data
Related structure data | 7q84SC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 75753.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACOX1, ACOX / Production host: Escherichia coli (E. coli) / References: acyl-CoA oxidase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.22 Å3/Da / Density % sol: 44.62 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop Details: 12.5 % PEG 8000, 0.09 M ammonium sulfate, 0.05 M sodium cacodylate (pH 6.0) + Soaking in 0.5 mM FAD |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→47.84 Å / Num. obs: 79500 / % possible obs: 99.85 % / Redundancy: 7.3 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.04 / Rrim(I) all: 0.11 / Net I/σ(I): 16.77 |
Reflection shell | Resolution: 2.09→2.165 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.207 / Num. unique obs: 7854 / CC1/2: 0.639 / CC star: 0.883 / Rpim(I) all: 0.04 / Rrim(I) all: 0.11 / % possible all: 99.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7Q84 Resolution: 2.09→47.84 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.17 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 151.41 Å2 / Biso mean: 46.884 Å2 / Biso min: 18.5 Å2
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Refinement step | Cycle: final / Resolution: 2.09→47.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.144 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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