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- PDB-6ju1: p-Hydroxybenzoate hydroxylase Y385F mutant complexed with 3,4-dih... -

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Basic information

Entry
Database: PDB / ID: 6ju1
Titlep-Hydroxybenzoate hydroxylase Y385F mutant complexed with 3,4-dihydroxybenzoate
Components4-hydroxybenzoate 3-monooxygenase
KeywordsOXIDOREDUCTASE / Aromatic compound hydroxylase / flavin / FAD
Function / homology
Function and homology information


benzoate catabolic process / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / 3,4-DIHYDROXYBENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / 4-hydroxybenzoate 3-monooxygenase / p-hydroxybenzoate hydroxylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsYato, M. / Arakawa, T. / Yamada, C. / Fushinobu, S.
CitationJournal: Biochemistry / Year: 2019
Title: Understanding the Molecular Mechanism Underlying the High Catalytic Activity ofp-Hydroxybenzoate Hydroxylase Mutants for Producing Gallic Acid.
Authors: Moriwaki, Y. / Yato, M. / Terada, T. / Saito, S. / Nukui, N. / Iwasaki, T. / Nishi, T. / Kawaguchi, Y. / Okamoto, K. / Arakawa, T. / Yamada, C. / Fushinobu, S. / Shimizu, K.
History
DepositionApr 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxybenzoate 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,52611
Polymers46,5381
Non-polymers1,98810
Water7,170398
1
A: 4-hydroxybenzoate 3-monooxygenase
hetero molecules

A: 4-hydroxybenzoate 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,05322
Polymers93,0762
Non-polymers3,97720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9330 Å2
ΔGint-39 kcal/mol
Surface area30410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.866, 145.901, 86.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-407-

PG4

21A-408-

P33

31A-801-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 4-hydroxybenzoate 3-monooxygenase /


Mass: 46537.914 Da / Num. of mol.: 1 / Mutation: Y385F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pobA, DT376_03235 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: A0A367MFY2, UniProt: P20586*PLUS, 4-hydroxybenzoate 3-monooxygenase

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Non-polymers , 7 types, 408 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID / Protocatechuic acid


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#7: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.15 M KBr, 30% PEG 2000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.29 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 14, 2018
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.29 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 59096 / % possible obs: 99.6 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 28.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.914 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.751 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1IUV

1iuv


Resolution: 1.6→40.13 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.814 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18594 2941 5 %RANDOM
Rwork0.15803 ---
obs0.15945 56131 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.047 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.6→40.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 125 398 3639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133304
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173099
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.6544461
X-RAY DIFFRACTIONr_angle_other_deg1.4831.5887140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.80319.738191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68515542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2741538
X-RAY DIFFRACTIONr_chiral_restr0.0890.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023665
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02754
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9522.121571
X-RAY DIFFRACTIONr_mcbond_other1.9272.1191570
X-RAY DIFFRACTIONr_mcangle_it2.6463.1741962
X-RAY DIFFRACTIONr_mcangle_other2.6513.1761963
X-RAY DIFFRACTIONr_scbond_it3.1842.5131733
X-RAY DIFFRACTIONr_scbond_other3.1842.5131733
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8093.612500
X-RAY DIFFRACTIONr_long_range_B_refined6.44326.5123822
X-RAY DIFFRACTIONr_long_range_B_other6.31525.7913732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 215 -
Rwork0.311 3845 -
obs--94.05 %

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