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- PDB-8y2s: P-hydroxybenzoate hydroxylase complexed with 4-hydroxy-3-methylbe... -

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Basic information

Entry
Database: PDB / ID: 8y2s
TitleP-hydroxybenzoate hydroxylase complexed with 4-hydroxy-3-methylbenzoic acid
Components4-hydroxybenzoate 3-monooxygenase
KeywordsOXIDOREDUCTASE / p-hydroxybenzoate hydroxylase / 4-hydroxy-3-methylbenzoic acid
Function / homology
Function and homology information


benzoate catabolic process / 4-hydroxybenzoate 3-monooxygenase / 4-hydroxybenzoate 3-monooxygenase activity / FAD binding
Similarity search - Function
4-hydroxybenzoate 3-monooxygenase / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / 4-hydroxybenzoate 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHara, K. / Hashimoto, H. / Matsushita, T. / Kishimoto, S. / Watanabe, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2024
Title: Functional Enhancement of Flavin-Containing Monooxygenase through Machine Learning Methodology
Authors: Matsushita, T. / Kishimoto, S. / Hara, K. / Hashimoto, H. / Yamaguchi, H. / Saito, Y. / Watanabe, K.
History
DepositionJan 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,2103
Polymers45,2731
Non-polymers9382
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-8 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.251, 141.900, 89.571
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-674-

HOH

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Components

#1: Protein 4-hydroxybenzoate 3-monooxygenase /


Mass: 45272.543 Da / Num. of mol.: 1 / Mutation: V47M, L199N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pobA, CGU42_30330, GNQ48_09340, IPC737_09120 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A233TK29, 4-hydroxybenzoate 3-monooxygenase
#2: Chemical ChemComp-A1LXW / 3-methyl-4-oxidanyl-benzoic acid


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 3350, 0.24 M sodium citrate, 0.1 M Bis-trispropane pH6.5, 80 mM 4-hydroxy-3-methylbenzoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→44.785 Å / Num. obs: 31316 / % possible obs: 99.49 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05704 / Net I/σ(I): 19
Reflection shellResolution: 2→2.071 Å / Redundancy: 7 % / Rmerge(I) obs: 0.8672 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 3058 / CC1/2: 0.869 / % possible all: 99.29

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.785 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 1995 6.38 %
Rwork0.2177 --
obs0.2199 31289 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→44.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 64 80 3244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033234
X-RAY DIFFRACTIONf_angle_d0.7114386
X-RAY DIFFRACTIONf_dihedral_angle_d14.5651193
X-RAY DIFFRACTIONf_chiral_restr0.026472
X-RAY DIFFRACTIONf_plane_restr0.002563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.36041390.33572045X-RAY DIFFRACTION99
2.05-2.10540.37881410.31142054X-RAY DIFFRACTION99
2.1054-2.16740.31281400.29052056X-RAY DIFFRACTION99
2.1674-2.23740.30311420.28572075X-RAY DIFFRACTION99
2.2374-2.31730.31741390.28722062X-RAY DIFFRACTION99
2.3173-2.41010.311410.26112083X-RAY DIFFRACTION99
2.4101-2.51980.25851400.24982048X-RAY DIFFRACTION99
2.5198-2.65260.26031420.24792100X-RAY DIFFRACTION99
2.6526-2.81880.26061420.24092077X-RAY DIFFRACTION100
2.8188-3.03640.28691430.242106X-RAY DIFFRACTION100
3.0364-3.34180.26361450.22822113X-RAY DIFFRACTION100
3.3418-3.82520.22231430.20052106X-RAY DIFFRACTION99
3.8252-4.81840.23381460.17192146X-RAY DIFFRACTION100
4.8184-44.7850.21661520.18682223X-RAY DIFFRACTION99

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