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Yorodumi- PDB-1cc4: PHE161 AND ARG166 VARIANTS OF P-HYDROXYBENZOATE HYDROXYLASE. IMPL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cc4 | ||||||
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Title | PHE161 AND ARG166 VARIANTS OF P-HYDROXYBENZOATE HYDROXYLASE. IMPLICATIONS FOR NADPH RECOGNITION AND STRUCTURAL STABILITY. | ||||||
Components | PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE) | ||||||
Keywords | OXIDOREDUCTASE / HYDROXYBENZOATE | ||||||
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 Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Eppink, M.H.M. / Bunthof, C. / Schreuder, H.A. / Van Berkel, W.J.H. | ||||||
Citation | Journal: Febs Lett. / Year: 1999 Title: Phe161 and Arg166 variants of p-hydroxybenzoate hydroxylase. Implications for NADPH recognition and structural stability. Authors: Eppink, M.H. / Bunthol, C. / Schreuder, H.A. / van Berkel, W.J. #1: Journal: Protein Sci. / Year: 1994 Title: Crystal structure of p-hydroxybenzoate hydroxylase reconstituted with the modified FAD present in alcohol oxidase from methylotrophic yeasts: evidence for an arabinoflavin. Authors: van Berkel, W.J. / Eppink, M.H. / Schreuder, H.A. #2: Journal: Biochemistry / Year: 1994 Title: Crystal structures of wild-type p-hydroxybenzoate hydroxylase complexed with 4-aminobenzoate,2,4-dihydroxybenzoate, and 2-hydroxy-4-aminobenzoate and of the Tyr222Ala mutant complexed with 2- ...Title: Crystal structures of wild-type p-hydroxybenzoate hydroxylase complexed with 4-aminobenzoate,2,4-dihydroxybenzoate, and 2-hydroxy-4-aminobenzoate and of the Tyr222Ala mutant complexed with 2-hydroxy-4-aminobenzoate. Evidence for a proton channel and a new binding mode of the flavin ring. Authors: Schreuder, H.A. / Mattevi, A. / Obmolova, G. / Kalk, K.H. / Hol, W.G. / van der Bolt, F.J. / van Berkel, W.J. #3: Journal: Proteins / Year: 1992 Title: Crystal structure of the reduced form of p-hydroxybenzoate hydroxylase refined at 2.3 A resolution. Authors: Schreuder, H.A. / van der Laan, J.M. / Swarte, M.B. / Kalk, K.H. / Hol, W.G. / Drenth, J. #4: Journal: Febs Lett. / Year: 1990 Title: Engineering of microheterogeneity-resistant p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens. Authors: Eschrich, K. / van Berkel, W.J. / Westphal, A.H. / de Kok, A. / Mattevi, A. / Obmolova, G. / Kalk, K.H. / Hol, W.G. #5: Journal: J.Mol.Biol. / Year: 1989 Title: Crystal structure of the p-hydroxybenzoate hydroxylase-substrate complex refined at 1.9 A resolution. Analysis of the enzyme-substrate and enzyme-product complexes. Authors: Schreuder, H.A. / Prick, P.A. / Wierenga, R.K. / Vriend, G. / Wilson, K.S. / Hol, W.G. / Drenth, J. #6: Journal: Biochemistry / Year: 1989 Title: The coenzyme analogue adenosine 5-diphosphoribose displaces FAD in the active site of p-hydroxybenzoate hydroxylase. An x-ray crystallographic investigation. Authors: van der Laan, J.M. / Schreuder, H.A. / Swarte, M.B. / Wierenga, R.K. / Kalk, K.H. / Hol, W.G. / Drenth, J. #7: Journal: J.Mol.Biol. / Year: 1988 Title: Crystal structure of p-hydroxybenzoate hydroxylase complexed with its reaction product 3,4-dihydroxybenzoate. Authors: Schreuder, H.A. / van der Laan, J.M. / Hol, W.G. / Drenth, J. #8: Journal: J.Mol.Biol. / Year: 1979 Title: Crystal structure of p-hydroxybenzoate hydroxylase. Authors: Wierenga, R.K. / de Jong, R.J. / Kalk, K.H. / Hol, W.G. / Drenth, J. #9: Journal: J.Biol.Chem. / Year: 1975 Title: Crystallization and preliminary x-ray investigation of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens. Authors: Drenth, J. / Hol, W.G. / Wierenga, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cc4.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cc4.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 1cc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cc4_validation.pdf.gz | 706.9 KB | Display | wwPDB validaton report |
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Full document | 1cc4_full_validation.pdf.gz | 709.7 KB | Display | |
Data in XML | 1cc4_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 1cc4_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/1cc4 ftp://data.pdbj.org/pub/pdb/validation_reports/cc/1cc4 | HTTPS FTP |
-Related structure data
Related structure data | 1cc6C 1pbeS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44288.414 Da / Num. of mol.: 1 / Mutation: F161A, C116S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: TG2 / Gene: POBA / Plasmid: PUC9 / Gene (production host): POBA / Production host: Escherichia coli (E. coli) / Strain (production host): TG2 References: UniProt: P00438, 4-hydroxybenzoate 3-monooxygenase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-PHB / |
#4: 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: 2.7 Å3/Da / Density % sol: 53.04 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Eppink, M.H.M., (1995) Eur. J. Biochem., 231, 157. | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Nov 15, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→8 Å / Num. all: 27343 / Num. obs: 27343 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 4.9 / Net I/σ(I): 12 |
Reflection | *PLUS Rmerge(I) obs: 0.049 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PBE Resolution: 2→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 27.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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