[English] 日本語
Yorodumi- PDB-6ain: Crystal structure of p-nitrophenol 4-monooxygenase PnpA from Pseu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ain | ||||||
---|---|---|---|---|---|---|---|
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 / FLAVIN-ADENINE DINUCLEOTIDE / PnpA Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ain.cif.gz | 168.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ain.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ain.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ain_validation.pdf.gz | 785.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ain_full_validation.pdf.gz | 798.4 KB | Display | |
Data in XML | 6ain_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 6ain_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/6ain ftp://data.pdbj.org/pub/pdb/validation_reports/ai/6ain | HTTPS FTP |
-Related structure data
Related structure data | 6aioC 3ihgS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 9 - 402 / Label seq-ID: 9 - 402
|
-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: Chemical | ChemComp-FAD / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.08 % |
---|---|
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, 0.01mM FAD, 0.5mM PNP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2.48→30 Å / Num. obs: 32252 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 19.37 |
Reflection shell | Resolution: 2.48→2.57 Å / Rmerge(I) obs: 0.493 / Num. unique obs: 3154 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IHG Resolution: 2.48→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.376 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.521 / ESU R Free: 0.281 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.655 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.48→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|