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Yorodumi- PDB-4qiu: Crystal structure of Nitroalkane Oxidase from Pseudomonas aerugin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qiu | ||||||
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Title | Crystal structure of Nitroalkane Oxidase from Pseudomonas aeruginosa in Mutant complex form | ||||||
Components | Nitronate monooxygenase family protein | ||||||
Keywords | OXIDOREDUCTASE / TIM barrel / FMN / 1NP | ||||||
Function / homology | Function and homology information nitroalkane oxidase / : / nitronate monooxygenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å | ||||||
Authors | Chi, Y.M. / Lee, J.H. | ||||||
Citation | Journal: To be Published Title: Crystal structures and reaction mechanisms of nitroalkane oxidase (NAO) from Pseudomonas aeruginosa Authors: Chi, Y.M. / Lee, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qiu.cif.gz | 159.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qiu.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 4qiu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qiu_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4qiu_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4qiu_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 4qiu_validation.cif.gz | 52.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/4qiu ftp://data.pdbj.org/pub/pdb/validation_reports/qi/4qiu | HTTPS FTP |
-Related structure data
Related structure data | 4qisC 4qitC 3bw2S 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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-Components
#1: Protein | Mass: 37483.965 Da / Num. of mol.: 2 / Mutation: H183C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO581 / Gene: M801_4200 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: T2E9U5, UniProt: A0A0M3KKW2*PLUS, nitroalkane oxidase #2: Chemical | #3: Chemical | #4: 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: 2.3 Å3/Da / Density % sol: 46.47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% P550MME_P20K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 5, 2012 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→34.765 Å / Num. all: 133657 / Num. obs: 130396 / % possible obs: 97.56 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 13.76 Å2 |
Reflection shell | Resolution: 1.4→1.45 Å / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BW2 Resolution: 1.401→34.765 Å / FOM work R set: 0.8704 / SU ML: 0.16 / σ(F): 1.48 / Phase error: 20.95 / 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: 59.98 Å2 / Biso mean: 18.72 Å2 / Biso min: 6.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.401→34.765 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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