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- PDB-1pdh: CRYSTAL STRUCTURE OF P-HYDROXYBENZOATE HYDROXYLASE RECONSTITUTED ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pdh | ||||||
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Title | CRYSTAL STRUCTURE OF P-HYDROXYBENZOATE HYDROXYLASE RECONSTITUTED WITH THE MODIFIED FAD PRESENT IN ALCOHOL OXIDASE FROM METHYLOTROPHIC YEASTS: EVIDENCE FOR AN ARABINOFLAVIN | ||||||
![]() | P-HYDROXYBENZOATE HYDROXYLASE | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() | ||||||
![]() | Schreuder, H.A. / Eppink, M.H.M. / Van Berkel, W.J.H. | ||||||
![]() | ![]() 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. #1: ![]() Title: Crystal Structure of Wild-Type P-Hydroxybenzoate Hydroxylase Complexed with 4-Aminobenzoate, 2,4-Dihydroxybenzoate and 2-Hydroxy-4-Aminobenzoate. Evidence for a Proton Channel and a New ...Title: Crystal Structure of Wild-Type P-Hydroxybenzoate Hydroxylase Complexed with 4-Aminobenzoate, 2,4-Dihydroxybenzoate and 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.J. / Van Der Bolt, F. / Van Berkel, W.J.H. #2: ![]() Title: Crystal Structure of the Reduced Form of P-Hydroxybenzoate Hydroxylase Refine at 2.3 Angstroms Resolution Authors: Schreuder, H.A. / Van Der Laan, J.M. / Swarte, M.B.A. / Kalk, K.H. / Hol, W.G.J. / Drenth, J. #3: ![]() Title: Crystal Structure of the P-Hydroxybenzoate Hydroxylase-Substrate Complex Refined at 1.9 Angstroms Resolution Authors: Schreuder, H.A. / Prick, P.A.J. / Wierenga, R.K. / Vriend, G. / Wilson, K.S. / Hol, W.G.J. / Drenth, J. #4: ![]() Title: Analysis of the Active Site of the Flavoprotein P-Hydroxybenzoate Hydroxylase and Some Ideas with Respect to its Reaction Mechanism Authors: Schreuder, H.A. / Hol, W.G.J. / Drenth, J. #5: ![]() Title: The Coenzyme Analogue Adenosine 5-Diphosphoribose Displaces the Fad from the Active Site of P-Hydroxybenzoate Hydroxylase. An X-Ray Crystallographic Investigation Authors: Van Der Laan, J.M. / Schreuder, H.A. / Swarte, M.B.A. / Wierenga, R.K. / Kalk, K.H. / Hol, W.G.J. / Drenth, J. #6: ![]() Title: The Influence of Purification and Protein Heterogeneity on the Crystallization of P-Hydroxybenzoate Hydroxylase Authors: Van Der Laan, J.M. / Swarte, M.B.A. / Groendijk, H. / Hol, W.G.J. / Drenth, J. #7: ![]() 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.J. / Drenth, J. #8: ![]() Title: Molecular Modeling Reveals the Possible Importance of a Carbonyl Oxygen Binding Pocket for the Catalytic Mechanism of P-Hydroxybenzoate Hydroxylase Authors: Schreuder, H.A. / Hol, W.G.J. / Drenth, J. #9: ![]() Title: Comparison of the Three-Dimensional Protein and Nucleotide Structure of the Fad-Binding Domain of P-Hydroxybenzoate Hydroxylase with the Fad-as Well as Nadph-Binding Domains of Glutathione Reductase Authors: Wierenga, R.K. / Drenth, J. / Schultz, G.E. #10: ![]() Title: Crystal Structure of P-Hydroxybenzoate Hydroxylase Authors: Wierenga, R.K. / De Jong, R.J. / Kalk, K.H. / Hol, W.G.J. / Drenth, J. #11: ![]() Title: Crystallization and Preliminary X-Ray Investigation of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens Authors: Drenth, J. / Hol, W.G.J. / Wierenga, R.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.4 KB | Display | ![]() |
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PDB format | ![]() | 74.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 707.8 KB | Display | ![]() |
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Full document | ![]() | 710.7 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 275 |
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Components
#1: Protein | Mass: 44380.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() References: UniProt: P00438, 4-hydroxybenzoate 3-monooxygenase |
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#2: Chemical | ChemComp-FAS / |
#3: Chemical | ChemComp-PHB / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.21 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.1→8 Å / Num. obs: 26407 / % possible obs: 97.2 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Num. obs: 26934 / Num. measured all: 102196 / Rmerge(I) obs: 0.069 |
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Processing
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Refinement | Rfactor Rwork: 0.179 / Rfactor obs: 0.179 / Highest resolution: 2.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.1 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 26407 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |