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- PDB-1bkw: p-Hydroxybenzoate hydroxylase (phbh) mutant with cys116 replaced ... -

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Basic information

Entry
Database: PDB / ID: 1bkw
Titlep-Hydroxybenzoate hydroxylase (phbh) mutant with cys116 replaced by ser (c116s) and arg44 replaced by lys (r44k), in complex with fad and 4-hydroxybenzoic acid
ComponentsPROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)
KeywordsOXIDOREDUCTASE / 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEppink, M.H. / Schreuder, H.A. / Van Berkel, W.J.
Citation
Journal: Eur.J.Biochem. / Year: 1995
Title: Structure and function of mutant Arg44Lys of 4-hydroxybenzoate hydroxylase implications for NADPH binding.
Authors: Eppink, M.H. / 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 Methyloprophic 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 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 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 Angstroms 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 the 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, 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 Angstroms 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.J. / Wierenga, R.K.
History
DepositionJul 13, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 22, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2603
Polymers44,3361
Non-polymers9242
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)
hetero molecules

A: PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5206
Polymers88,6732
Non-polymers1,8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6300 Å2
ΔGint-32 kcal/mol
Surface area30470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.700, 146.400, 88.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)


Mass: 44336.492 Da / Num. of mol.: 1 / Mutation: R44K, C116S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / 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 / 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.: 243 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 7
Details: 39% AMMONIUMSULFATE, 100 MM SODIUM PHOSPHATE, 0.04 MM FAD, 0.15 MM EDTA, 60 MM SODIUM SULFITE, 1 MM P-HYDROXYBENZOATE, pH 7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
2100 mMpotassium phosphate1droppH7.0
339 %satammonium sulfate1reservoir
40.14 mMFAD1reservoir
50.15 mMEDTA1reservoir
61 mM4-hydroxybenzoate1reservoir
760 mMsodium sulfite1reservoir
8100 mMpotassium phosphate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 15, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→8 Å / Num. obs: 23336 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.068 / Net I/σ(I): 12
Reflection
*PLUS
Num. measured all: 92992 / Rmerge(I) obs: 0.068

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLORmodel building
X-PLOR3.8refinement
XDSdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBE

1pbe


Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rwork0.182 --
obs0.182 23336 96.6 %
Displacement parametersBiso mean: 28.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 63 243 3402
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2FAD.PARFAD.TOP
X-RAY DIFFRACTION3WAT.PARPHB.TOP
X-RAY DIFFRACTION4WAT.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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