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Yorodumi- PDB-4irn: Crystal Structure of the Prolyl Acyl Carrier Protein Oxidase AnaB -
+Open data
-Basic information
Entry | Database: PDB / ID: 4irn | ||||||
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Title | Crystal Structure of the Prolyl Acyl Carrier Protein Oxidase AnaB | ||||||
Components | Prolyl-ACP dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Acyl CoA Dehydrogenase fold / Acyl-ACP Oxidase | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Oscillatoria sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Moncoq, K. / Mann, S. / Regad, L. / Mejean, A. / Ploux, O. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structure of the prolyl-acyl carrier protein oxidase involved in the biosynthesis of the cyanotoxin anatoxin-a. Authors: Moncoq, K. / Regad, L. / Mann, S. / Mejean, A. / Ploux, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4irn.cif.gz | 605 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4irn.ent.gz | 496.8 KB | Display | PDB format |
PDBx/mmJSON format | 4irn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/4irn ftp://data.pdbj.org/pub/pdb/validation_reports/ir/4irn | HTTPS FTP |
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-Related structure data
Related structure data | 1jqiS S: Starting model for refinement |
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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: 46605.234 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oscillatoria sp. (bacteria) / Strain: PCC 6506 / Gene: anaB, OSCI_4070008 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus References: UniProt: C4NCB7, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors #2: Chemical | ChemComp-FAD / #3: 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: 2.16 Å3/Da / Density % sol: 43.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 24% PEG 4000, 100mM Tris-HCl pH 8.5 100mM MgCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 200 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→130.882 Å / Num. all: 76832 / Num. obs: 76832 / % possible obs: 99 % / Redundancy: 3.2 % / Biso Wilson estimate: 49.05 Å2 / Rsym value: 0.118 / Net I/σ(I): 9.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JQI Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.8675 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 101.17 Å2 / Biso mean: 29.5233 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.314 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20
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