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- PDB-1pbe: CRYSTAL STRUCTURE OF THE P-HYDROXYBENZOATE HYDROXYLASE-SUBSTRATE ... -

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Basic information

Entry
Database: PDB / ID: 1pbe
TitleCRYSTAL STRUCTURE OF THE P-HYDROXYBENZOATE HYDROXYLASE-SUBSTRATE COMPLEX REFINED AT 1.9 ANGSTROMS RESOLUTION. ANALYSIS OF THE ENZYME-SUBSTRATE AND ENZYME-PRODUCT COMPLEXES
ComponentsP-HYDROXYBENZOATE HYDROXYLASE
KeywordsOXIDOREDUCTASE
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
4-hydroxybenzoate 3-monooxygenase / : / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...4-hydroxybenzoate 3-monooxygenase / : / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / P-HYDROXYBENZOIC ACID / p-hydroxybenzoate hydroxylase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsSchreuder, H.A. / Hol, W.G.J. / Drenth, J.
Citation
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.
#1: Journal: Proteins / Year: 1992
Title: Crystal Structure of the Reduced Form of P-Hydroxybenzoate Hydroxylase Refined 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.
#2: Journal: Eur.J.Biochem. / Year: 1989
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.
#3: 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.A. / Wierenga, R.K. / Kalk, K.H. / Hol, W.G.J. / Drenth, J.
#4: Journal: Biochemistry / Year: 1989
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: Journal: J.Biol.Chem. / Year: 1988
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.
#6: 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.J. / Drenth, J.
#7: Journal: J.Mol.Biol. / Year: 1983
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. / Schulz, G.E.
#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.J. / 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.J. / Wierenga, R.K.
History
DepositionJul 6, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3043
Polymers44,3811
Non-polymers9242
Water5,945330
1
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6086
Polymers88,7612
Non-polymers1,8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6310 Å2
ΔGint-31 kcal/mol
Surface area30220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.500, 145.800, 88.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: CIS PROLINE - PRO 275

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Components

#1: Protein P-HYDROXYBENZOATE HYDROXYLASE


Mass: 44380.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria)
References: UniProt: P00438, 4-hydroxybenzoate 3-monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal grow
*PLUS
Temperature: 4-20 ℃ / pH: 7.5 / Method: free interface diffusion method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
22 mMp-hydroxybenzoate1drop
30.04 mMFAD1drop
40.3 mMEDTA1drop
530 mMsodium sulphite1drop
60.1 Mphosphate1drop
770 %satammonium sulphate1reservoir
80.1 Mphosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Rmerge(I) obs: 0.126

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→6 Å / σ(F): 0 /
RfactorNum. reflection
obs0.156 31148
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 63 330 3491
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0390.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.7255
X-RAY DIFFRACTIONp_mcangle_it4.5145
X-RAY DIFFRACTIONp_scbond_it7.7527
X-RAY DIFFRACTIONp_scangle_it10.53510
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.1850.15
X-RAY DIFFRACTIONp_singtor_nbd0.1890.35
X-RAY DIFFRACTIONp_multtor_nbd0.2220.35
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2410.35
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS

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