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Yorodumi- PDB-6aio: Crystal structure of p-nitrophenol 4-monooxygenase PnpA from Pseu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aio | ||||||
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Title | Crystal structure of p-nitrophenol 4-monooxygenase PnpA from Pseudomonas putida DLL-E4 | ||||||
Components | PnpA | ||||||
Keywords | FLAVOPROTEIN / p-Nitrophenol 4-monooxygenase | ||||||
Function / homology | FAD-binding domain / FAD binding domain / monooxygenase activity / FAD binding / FAD/NAD(P)-binding domain superfamily / PnpA Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Chen, Q.Z. / Huang, Y. / Duan, Y.J. / Li, Z.K. / Liu, W.D. / Cui, Z.L. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 Title: Crystal structure of p-nitrophenol 4-monooxygenase PnpA from Pseudomonas putida DLL-E4: The key enzyme involved in p-nitrophenol degradation. Authors: Chen, Q.Z. / Huang, Y. / Duan, Y.J. / Li, Z.K. / Cui, Z.L. / Liu, W.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aio.cif.gz | 175.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aio.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 6aio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aio_validation.pdf.gz | 443.9 KB | Display | wwPDB validaton report |
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Full document | 6aio_full_validation.pdf.gz | 453.6 KB | Display | |
Data in XML | 6aio_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 6aio_validation.cif.gz | 52.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/6aio ftp://data.pdbj.org/pub/pdb/validation_reports/ai/6aio | HTTPS FTP |
-Related structure data
Related structure data | 6ainC 3ihgS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 46628.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: DLL-E4 / Gene: pnpA / Production host: Escherichia coli (E. coli) / References: UniProt: C6FI48 #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: 2.29 Å3/Da / Density % sol: 46.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10% isopropanol, 0.1M Tris-HCl, pH 8.5, 13.5 % (w/v) PEG 4000, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.5397 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5397 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→30 Å / Num. obs: 55036 / % possible obs: 99.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.09 |
Reflection shell | Resolution: 2.04→2.11 Å / Rmerge(I) obs: 0.095 / Num. unique obs: 5337 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IHG Resolution: 2.04→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.704 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.807 Å2
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Refinement step | Cycle: 1 / Resolution: 2.04→30 Å
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Refine LS restraints |
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