[English] 日本語
Yorodumi- PDB-1bgn: P-HYDROXYBENZOATE HYDROXYLASE (PHBH) MUTANT WITH CYS 116 REPLACED... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bgn | ||||||
---|---|---|---|---|---|---|---|
Title | P-HYDROXYBENZOATE HYDROXYLASE (PHBH) MUTANT WITH CYS 116 REPLACED BY SER (C116S) AND ARG 269 REPLACED BY THR (R269T), IN COMPLEX WITH FAD AND 4-HYDROXYBENZOIC ACID | ||||||
Components | P-HYDROXYBENZOATE HYDROXYLASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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. / Schreuder, H.A. / Van Berkel, W.J.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Interdomain binding of NADPH in p-hydroxybenzoate hydroxylase as suggested by kinetic, crystallographic and modeling studies of histidine 162 and arginine 269 variants. Authors: Eppink, M.H. / Schreuder, H.A. / van Berkel, W.J. #1: Journal: Eur.J.Biochem. / Year: 1998 Title: Lys42 and Ser42 Variants of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens Reveal that Arg42 is Essential for Nadph Binding Authors: Eppink, M.H. / Schreuder, H.A. / Van Berkel, W.J. #2: 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. #3: 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. #4: 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. #5: 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. #6: 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. #7: 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. #8: 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. #9: 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. #10: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bgn.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bgn.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 1bgn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bgn_validation.pdf.gz | 688.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1bgn_full_validation.pdf.gz | 693.1 KB | Display | |
Data in XML | 1bgn_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1bgn_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/1bgn ftp://data.pdbj.org/pub/pdb/validation_reports/bg/1bgn | HTTPS FTP |
-Related structure data
Related structure data | 1bgjC 1pbeS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 44308.414 Da / Num. of mol.: 1 / Mutation: C116S, R269T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / 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 |
---|---|
#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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 Details: 39% AMMONIUMSULFATE, 100 MM SODIUM PHOSPHATE, 0.04 MM FAD, 0.15 MM EDTA, 30 MM SODIUM SULFITE, 1 MM P-HYDROXYBENZOATE, pH 7.0 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 280 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→8 Å / Num. obs: 26122 / % possible obs: 92.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.054 / Rsym value: 0.067 |
Reflection | *PLUS Rmerge(I) obs: 0.045 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PBE Resolution: 2→8 Å /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|