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Yorodumi- PDB-1k0j: Pseudomonas aeruginosa phbh R220Q in complex with NADPH and free ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k0j | ||||||
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Title | Pseudomonas aeruginosa phbh R220Q in complex with NADPH and free of p-OHB | ||||||
Components | P-HYDROXYBENZOATE HYDROXYLASE | ||||||
Keywords | HYDROLASE / phbh / FAD / NADPH | ||||||
Function / homology | Function and homology information 4-hydroxybenzoate 3-monooxygenase (NADPH) activity / 4-hydroxybenzoate 3-monooxygenase / 4-hydroxybenzoate 3-monooxygenase activity / benzoate catabolic process via hydroxylation / FAD binding / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wang, J. / Ortiz-Maldonado, M. / Entsch, B. / Ballou, D. / Gatti, D.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Protein and ligand dynamics in 4-hydroxybenzoate hydroxylase. Authors: Wang, J. / Ortiz-Maldonado, M. / Entsch, B. / Massey, V. / Ballou, D. / Gatti, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k0j.cif.gz | 97.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k0j.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 1k0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k0j_validation.pdf.gz | 555.6 KB | Display | wwPDB validaton report |
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Full document | 1k0j_full_validation.pdf.gz | 567.3 KB | Display | |
Data in XML | 1k0j_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 1k0j_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/1k0j ftp://data.pdbj.org/pub/pdb/validation_reports/k0/1k0j | HTTPS FTP |
-Related 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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Details | The enzyme is a dimer in solution. But only one monomer is present in the asymmetric unit. |
-Components
#1: Protein | Mass: 44353.484 Da / Num. of mol.: 1 / Mutation: R220Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: bl21 / Production host: Escherichia coli (E. coli) References: UniProt: P20586, 4-hydroxybenzoate 3-monooxygenase | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-FAD / | #4: Chemical | ChemComp-NDP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.34 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM potassium phosphate, 0.05 mM glutathion, 30mM sodium sulfite 0.02mM FAD, 450mM ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 30 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2001 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→22.07 Å / Num. all: 19340 / Num. obs: 19340 / % possible obs: 81.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.13 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.726 / Num. unique all: 2016 / % possible all: 57.3 |
Reflection | *PLUS Num. obs: 20552 / % possible obs: 86.6 % / Num. measured all: 262880 / Rmerge(I) obs: 0.13 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→22.07 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 42.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→22.07 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 22 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.221 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 42.5 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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