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Yorodumi- PDB-7da9: Structure of 6-hydroxy-3-succinoyl-pyridine 3-monooxygenase (HspB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7da9 | ||||||
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Title | Structure of 6-hydroxy-3-succinoyl-pyridine 3-monooxygenase (HspB) from Pseudomonas putida S16 | ||||||
Components | 6-hydroxy-3-succinoylpyridine 3-monooxygenase HspB | ||||||
Keywords | OXIDOREDUCTASE / monooxygenase | ||||||
Function / homology | 6-hydroxy-3-succinoylpyridine 3-monooxygenase / nicotine catabolic process / alkaloid metabolic process / FAD-binding domain / FAD binding domain / FAD binding / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / 6-hydroxy-3-succinoylpyridine 3-monooxygenase HspB Function and homology information | ||||||
Biological species | Pseudomonas putida S16 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.108 Å | ||||||
Authors | Liu, G.Q. / Liu, G.Q. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of 6-hydroxy-3-succinoyl-pyridine 3-monooxygenase (HspB) from Pseudomonas putida S16 Authors: Liu, G.Q. / Liu, G.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7da9.cif.gz | 330.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7da9.ent.gz | 268.5 KB | Display | PDB format |
PDBx/mmJSON format | 7da9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/7da9 ftp://data.pdbj.org/pub/pdb/validation_reports/da/7da9 | HTTPS FTP |
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-Related structure data
Related structure data | 6ainS 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: 44023.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida S16 (bacteria) / Strain: S16 / Gene: hspB, PPS_4061 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: F8G0M4, 6-hydroxy-3-succinoylpyridine 3-monooxygenase #2: 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: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 25% PEG4000, 0.1 mol/L Bis-Tris pH 8.0, 0.2 mol/L MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 45977 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.993 / Net I/σ(I): 21.13 |
Reflection shell | Resolution: 2.1→2.14 Å / Num. unique obs: 2290 / CC1/2: 0.708 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AIN Resolution: 2.108→30.563 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.91 / 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: 79.17 Å2 / Biso mean: 28.7832 Å2 / Biso min: 10.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.108→30.563 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 11.269 Å / Origin y: -14.2177 Å / Origin z: -11.4467 Å
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Refinement TLS group |
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