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

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Basic information

Entry
Database: PDB / ID: 1iux
TitleP-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-4-HYDROXYBENZOATE AT PH 9.4
ComponentsP-HYDROXYBENZOATE HYDROXYLASE
KeywordsOXIDOREDUCTASE / AROMATIC HYDROCARBONS CATABOLISM / OXIDOREDUCATASE
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 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 1.0Jul 11, 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
Water3,387188
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 area6460 Å2
ΔGint-25 kcal/mol
Surface area30460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.730, 146.370, 88.050
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 9.4 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.: 188 / 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: 2.61 Å3/Da / Density % sol: 31.9 %
Crystal growpH: 9.4 / Details: pH 9.4
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: XUONG-HAMLIN MULTIWIRE / 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→15 Å / Num. obs: 31069 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 7.58 % / Rmerge(I) obs: 0.295 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.15 Å / Redundancy: 4.55 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 0.0105 / % possible all: 94.08

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata reduction
SDMSdata scaling
X-PLOR3.1phasing
RefinementResolution: 2→15 Å / σ(F): 0
Details: THE SEGMENT PRO 293 - ALA 296 IS PRESENT IN TWO CONFORMATIONS. CYS 116: MODIFIED CYSTEINE WITH ADDITIONAL ELECTRON DENSITY NEAR THE SULFUR AT X=5.47 Y=107.86 Z=71.44. THE TYPE OF CHEMICAL ...Details: THE SEGMENT PRO 293 - ALA 296 IS PRESENT IN TWO CONFORMATIONS. CYS 116: MODIFIED CYSTEINE WITH ADDITIONAL ELECTRON DENSITY NEAR THE SULFUR AT X=5.47 Y=107.86 Z=71.44. THE TYPE OF CHEMICAL MODIFICATION CANNOT BE UNAMBIGUOUSLY DETERMINED FROM THE ELECTRON DENSITY. SIDE CHAIN OF RESIDUES 136, 173, 393, 394 NOT ORDERED. THE THE MODEL IS DERIVED FROM A COMBINATION OF FIT TO RESIDUAL DENSITY AND ENERGY MINIMIZATION.
RfactorNum. reflection% reflection
Rwork0.1735 --
obs0.1735 31069 98.3 %
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 63 188 3375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.582
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.02
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.384
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 / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.029
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.384

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