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- PDB-1ius: P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-AMINOBENZOATE AT PH 5.0 -

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Basic information

Entry
Database: PDB / ID: 1ius
TitleP-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-AMINOBENZOATE AT PH 5.0
ComponentsP-HYDROXYBENZOATE HYDROXYLASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


4-hydroxybenzoate 3-monooxygenase / 4-hydroxybenzoate 3-monooxygenase [NADPH] activity / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 4-AMINOBENZOIC ACID / p-hydroxybenzoate hydroxylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 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-Dihydrobenzoate 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-Dihydrobenzoate 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.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 1.0Apr 3, 1996Provider: 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 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)45,3053
Polymers44,3831
Non-polymers9232
Water3,729207
1
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6106
Polymers88,7652
Non-polymers1,8454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6440 Å2
ΔGint-26 kcal/mol
Surface area30690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.710, 146.570, 88.390
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 / 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)
References: UniProt: P20586, 4-hydroxybenzoate 3-monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PAB / 4-AMINOBENZOIC ACID / 4-Aminobenzoic acid


Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growpH: 5 / Details: pH 5.0
Crystal
*PLUS
Density % sol: 34.8 %
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
34 mMp-ABA11
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 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Details: 0.5 MM COLLIMATOR
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 6.81 % / Rmerge(I) obs: 0.302 / Net I/σ(I): 2.01
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / Num. obs: 23957 / % possible obs: 99.9 % / Redundancy: 8.34 % / Rmerge(I) obs: 0.113
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.35 Å / % possible obs: 99.9 % / Redundancy: 6.81 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.01

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→15 Å / σ(F): 0
Details: THE HYDROGEN BOND DISTANCE CUTOFF USED FOR THE TURNS IS 3.5 ANGSTROMS. THE CA(X) TO CA(X+4) DISTANCE IS LESS THAN 6.0 ANGSTROMS. THE ANGLES ARE FROM ROBSON AND GARNIER, (1986), 'INTRODUCTION ...Details: THE HYDROGEN BOND DISTANCE CUTOFF USED FOR THE TURNS IS 3.5 ANGSTROMS. THE CA(X) TO CA(X+4) DISTANCE IS LESS THAN 6.0 ANGSTROMS. THE ANGLES ARE FROM ROBSON AND GARNIER, (1986), 'INTRODUCTION TO PROTEINS AND PROTEIN ENGINEERING', ELSEVIER, AMSTERDAM. TYPE PHI2 PSI2 PHI3 PSI3 I -75(+-65) -30(+-40) -90(+-40) -15 TO 40 II -60(+-40) 120(+-40) 90(+-40) 0(+-40) III -75(+-65) -30(+-40) -60(+-40) -15 TO -70 I(PRIME) 75(+-65) 30(+-40) 90(+-40) -40 TO 15 II(PRIME) 60(+-40) -120(+-40) -90(+-40) 0(+-40) III(PRIME) 75(+-65) 30(+-40) 60(+-40) 15 TO 70 MODIFIED CYSTEINE WITH ADDITIONAL ELECTRON DENSITY NEAR THE SULFUR AT X=5.26, Y=107.89, Z=71.02 - CYS 116. THE TYPE OF CHEMICAL MODIFICATION CANNOT BE UNAMBIGUOUSLY DETERMINED FROM THE ELECTRON DENSITY THE SIDE CHAINS OF RESIDUES 135, 136, 146, 392, 393, 394 ARE NOT ORDERED. THE MODEL IS DERIVED FROM A COMBINATION OF FIT TO RESIDUAL DENSITY AND ENERGY MINIMIZATION.
RfactorNum. reflection
Rwork0.167 -
obs0.167 23957
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 63 207 3394
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_deg1.642
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.04
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.447
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.04
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.447

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