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Yorodumi- PDB-5o8p: The crystal structure of DfoA bound to FAD, the desferrioxamine b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o8p | ||||||
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Title | The crystal structure of DfoA bound to FAD, the desferrioxamine biosynthetic pathway cadaverine monooxygenase from the fire blight disease pathogen Erwinia amylovora | ||||||
Components | L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis | ||||||
Keywords | BIOSYNTHETIC PROTEIN / siderophore biosynthesis / cadaverine monooxygenase / NADP(H) / FAD | ||||||
Function / homology | L-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / cellular biosynthetic process / : / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis Function and homology information | ||||||
Biological species | Erwinia amylovora CFBP1430 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Salomone-Stagni, M. / Bartho, J.D. / Polsinelli, I. / Bellini, D. / Walsh, M.A. / Demitri, N. / Benini, S. | ||||||
Funding support | Italy, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2018 Title: A complete structural characterization of the desferrioxamine E biosynthetic pathway from the fire blight pathogen Erwinia amylovora. Authors: Salomone-Stagni, M. / Bartho, J.D. / Polsinelli, I. / Bellini, D. / Walsh, M.A. / Demitri, N. / Benini, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o8p.cif.gz | 185.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o8p.ent.gz | 147.5 KB | Display | PDB format |
PDBx/mmJSON format | 5o8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o8p_validation.pdf.gz | 709.1 KB | Display | wwPDB validaton report |
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Full document | 5o8p_full_validation.pdf.gz | 722.8 KB | Display | |
Data in XML | 5o8p_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 5o8p_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/5o8p ftp://data.pdbj.org/pub/pdb/validation_reports/o8/5o8p | HTTPS FTP |
-Related structure data
Related structure data | 5o5cC 5o7oC 5o8rC 4tlxS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 3 - 428 / Label seq-ID: 6 - 431
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-Components
#1: Protein | Mass: 50429.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erwinia amylovora CFBP1430 (bacteria) / Gene: dfoA, EAMY_3239 / Production host: Escherichia coli (E. coli) References: UniProt: D4I246, L-lysine N6-monooxygenase (NADPH) #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: 5.62 Å3/Da / Density % sol: 78.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M HEPES, 1.45 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→117.57 Å / Num. obs: 60324 / % possible obs: 99.99 % / Redundancy: 13.1 % / Rrim(I) all: 0.066 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.75→2.85 Å / Num. unique obs: 4397 / Rrim(I) all: 0.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4tlx Resolution: 2.75→117.57 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.941 / SU B: 24.081 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.221 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 44.819 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→117.57 Å
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Refine LS restraints |
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