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- PDB-1phh: CRYSTAL STRUCTURE OF P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 1phh
TitleCRYSTAL STRUCTURE OF P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH ITS REACTION PRODUCT 3,4-DIHYDROXYBENZOATE
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
3,4-DIHYDROXYBENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / p-hydroxybenzoate hydroxylase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsSchreuder, H.A. / Drenth, J.
Citation
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.
#1: Journal: Eur.J.Biochem. / Year: 1983
Title: P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens. 2. Fitting of the Amino-Acid Sequence to the Tertiary Structure
Authors: Weijer, W.J. / Hofsteenge, J. / Beintema, J.J. / Wierenga, R.K. / Drenth, J.
#2: Journal: Eur.J.Biochem. / Year: 1983
Title: P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens. 1. Completion of the Elucidation of the Primary Structure
Authors: Hofsteenge, J. / Weijer, W.J. / Jekel, P.A. / Beintema, J.J.
#3: 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.
#4: Journal: Eur.J.Biochem. / Year: 1980
Title: Primary and Tertiary Structure Studies of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens. Isolation and Alignment of the Cnbr Peptides. Interactions of the Protein with Flavin Adenine Dinucleotide
Authors: Hofsteenge, J. / Vereijken, J.M. / Weijer, W.J. / Beintema, J.J. / Wierenga, R.K. / Drenth, J.
#5: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structure of P-Hydroxybenzoate Hydroxylase
Authors: Wierenga, R.K. / Dejong, R.J. / Kalk, K.H. / Hol, W.G.J. / Drenth, J.
#6: Journal: J.Biol.Chem. / Year: 1975
Title: Crystallization and Preliminary X-Ray Investigation of P-Hydrobenzoate Hydroxylase from Pseudomonas Fluorescens
Authors: Drenth, J. / Hol, W.G.J. / Wierenga, R.K.
History
DepositionNov 4, 1987Processing site: BNL
Revision 1.0Apr 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3203
Polymers44,3811
Non-polymers9402
Water4,918273
1
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6406
Polymers88,7612
Non-polymers1,8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6350 Å2
ΔGint-26 kcal/mol
Surface area31600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.900, 146.300, 88.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: RESIDUE 275 IS A CIS-PROLINE.

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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-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal grow
*PLUS
Temperature: 4-20 ℃ / pH: 7.5 / Method: batch method
Details: took method of Drenth et al., 1975 from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein11
22 mMp-hydroxybezoate11
30.04 mMFAD11
40.3 mMEDTA11
50.2 mMreduced glutathione11
630 mMsodium sulfate11
70.1 Mpotassium phosphate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 15546 / Num. measured all: 103934 / Rmerge F obs: 0.055

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.193 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 64 273 3462
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
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
Lowest resolution: 6 Å / Num. reflection obs: 14339 / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_dihedral_angle_d32.1
X-RAY DIFFRACTIONp_dihedral_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_plane_restr0.020.01
X-RAY DIFFRACTIONp_chiral_restr0.150.181
X-RAY DIFFRACTIONp_mcbond_it21.106
X-RAY DIFFRACTIONp_scbond_it3.52.991
X-RAY DIFFRACTIONp_mcangle_it21.798
X-RAY DIFFRACTIONp_scangle_it54.298

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