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Yorodumi- PDB-6xbb: Crystal structure of Streptomyces sviceus SsDesB in complex with NADP+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xbb | ||||||
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Title | Crystal structure of Streptomyces sviceus SsDesB in complex with NADP+ | ||||||
Components | Monooxigenase | ||||||
Keywords | FLAVOPROTEIN / N-hydroxylase / flavin-dependent monooygenase / desferrioxamine biosynthesis | ||||||
Function / homology | Function and homology information L-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / cellular biosynthetic process / organonitrogen compound biosynthetic process Similarity search - Function | ||||||
Biological species | Streptomyces sviceus ATCC 29083 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.366 Å | ||||||
Authors | Lountos, G.T. / Giddings, L.A. / Waugh, D.S. | ||||||
Citation | Journal: Plos One / Year: 2021 Title: Characterization of a broadly specific cadaverine N-hydroxylase involved in desferrioxamine B biosynthesis in Streptomyces sviceus. Authors: Giddings, L.A. / Lountos, G.T. / Kim, K.W. / Brockley, M. / Needle, D. / Cherry, S. / Tropea, J.E. / Waugh, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xbb.cif.gz | 699.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xbb.ent.gz | 577.8 KB | Display | PDB format |
PDBx/mmJSON format | 6xbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/6xbb ftp://data.pdbj.org/pub/pdb/validation_reports/xb/6xbb | HTTPS FTP |
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-Related structure data
Related structure data | 6xbcC 5o8pS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48241.914 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sviceus ATCC 29083 (bacteria) Gene: SSEG_08523 / Plasmid: pGL3070 / Production host: Escherichia coli (E. coli) / References: UniProt: B5HNG5 #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-NAP / #4: 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: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 0.2M NaCl, 20% PEG3350, 10 mM sarcosine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.366→50 Å / Num. obs: 139487 / % possible obs: 96.3 % / Redundancy: 3.7 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.089 / Rrim(I) all: 0.103 / Rsym value: 0.053 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.366→2.41 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / Num. unique obs: 6996 / CC1/2: 0.729 / CC star: 0.918 / Rpim(I) all: 0.418 / Rrim(I) all: 0.809 / Rsym value: 0.692 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5o8p Resolution: 2.366→37.016 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.18 / 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: 83.13 Å2 / Biso mean: 35.2461 Å2 / Biso min: 11.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.366→37.016 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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