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- PDB-1iuv: P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-4-HYDROXYBENZOATE ... -

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Basic information

Entry
Database: PDB / ID: 1iuv
TitleP-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-4-HYDROXYBENZOATE AT PH 5.0
ComponentsP-HYDROXYBENZOATE HYDROXYLASE
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / FLAVOPROTEIN
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 / oxidoreductase activity
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 aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsGatti, D.L. / Entsch, B. / Ballou, D.P. / Ludwig, M.L.
Citation
Journal: Biochemistry / Year: 1996
Title: pH-dependent structural changes in the active site of p-hydroxybenzoate hydroxylase point to the importance of proton and water movements during catalysis.
Authors: Gatti, D.L. / Entsch, B. / Ballou, D.P. / Ludwig, M.L.
#1: 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.
#2: Journal: Biochemistry / Year: 1994
Title: Crystal Structures of Mutant Pseudomonas Aeruginosa P-Hydroxybenzoate Hydroxylases: The Tyr201Phe, Tyr385Phe, and Asn300Asp Variants
Authors: Lah, M.S. / Palfey, B.A. / Schreuder, H.A. / Ludwig, M.L.
#3: Journal: J.Biol.Chem. / Year: 1991
Title: Catalytic Function of Tyrosine Residues in Para-Hydroxybenzoate Hydroxylase as Determined by the Study of Site-Directed Mutants
Authors: Entsch, B. / Palfey, B.A. / Ballou, D.P. / Massey, V.
History
DepositionNov 22, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / 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 7, 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)45,3063
Polymers44,3831
Non-polymers9242
Water2,486138
1
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6126
Polymers88,7652
Non-polymers1,8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6440 Å2
ΔGint-27 kcal/mol
Surface area30500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.650, 146.430, 88.770
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 P-HYDROXYBENZOATE HYDROXYLASE / PHBH


Mass: 44382.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PH 5.0 STRUCTURE / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: POBA / Plasmid: PIE130 / Gene (production host): POBA / Production host: Escherichia coli (E. coli) / Strain (production host): JM105
References: UniProt: P20586, 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.: 138 / 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: 2.63 Å3/Da / Density % sol: 35.2 %
Crystal growpH: 5 / Details: pH 5.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4-23 ℃ / pH: 7.4 / Method: interface diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlPHBH110.005ml
20.1 Mpotassium phosphate11
32 mMp-OHB11
40.004 mMFAD11
50.2 mMglutathione11
671 %satammonium sulfate12
70.1 Mpotassium phosphate12

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceWavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Details: 0.5 MM COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 16343 / % possible obs: 99.31 % / Redundancy: 6.32 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 9
Reflection shellResolution: 2.5→2.65 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.21 / % possible all: 97.61

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
X-PLORphasing
RefinementResolution: 2.5→15 Å / σ(F): 0
Details: ASSIGNMENTS OF SECONDARY STRUCTURE ARE BASED ON DSSP OUTPUT (KABSCH AND SANDER, 1983). THERE IS A MODIFIED CYSTEINE WITH ADDITIONAL ELECTRON DENSITY NEAR THE SULFUR AT X=4.90 Y=106.61 Z=72. ...Details: ASSIGNMENTS OF SECONDARY STRUCTURE ARE BASED ON DSSP OUTPUT (KABSCH AND SANDER, 1983). THERE IS A MODIFIED CYSTEINE WITH ADDITIONAL ELECTRON DENSITY NEAR THE SULFUR AT X=4.90 Y=106.61 Z=72.18: CYS 116. THE TYPE OF CHEMICAL MODIFICATION CANNOT BE UNAMBIGUOUSLY DETERMINED FROM THE ELECTRON DENSITY. THE SIDE CHAINS OF RESIDUES 23, 136, 144, 173, 311, 321, 355, 391, 392, 393, AND 394 ARE NOT ORDERED. THE MODEL IS DERIVED FROM A COMBINATION OF FIT TO RESIDUAL DENSITY AND ENERGY MINIMIZATION.
RfactorNum. reflection% reflection
Rwork0.173 --
obs0.173 16343 99.31 %
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 63 138 3325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.667
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.98
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.472
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.98
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.472

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