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- PDB-8jqp: Protocatecuate hydroxylase from Xylophilus ampelinus complexed wi... -

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Basic information

Entry
Database: PDB / ID: 8jqp
TitleProtocatecuate hydroxylase from Xylophilus ampelinus complexed with 3,4-dihydroxybenzoate
Components4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
KeywordsOXIDOREDUCTASE / p-hydroxybenzoate hydroxylase / FAD / NADPH
Function / homology3,4-DIHYDROXYBENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / :
Function and homology information
Biological speciesXylophilus ampelinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFukushima, R. / Katsuki, N. / Fushinobu, S. / Takaya, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19H05679 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05687 Japan
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Protocatechuate hydroxylase is a novel group A flavoprotein monooxygenase with a unique substrate recognition mechanism.
Authors: Katsuki, N. / Fukushima, R. / Doi, Y. / Masuo, S. / Arakawa, T. / Yamada, C. / Fushinobu, S. / Takaya, N.
History
DepositionJun 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 3, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
B: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,51512
Polymers91,0632
Non-polymers2,45210
Water10,827601
1
B: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
hetero molecules

A: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,51512
Polymers91,0632
Non-polymers2,45210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area7600 Å2
ΔGint-30 kcal/mol
Surface area28930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.966, 65.074, 80.681
Angle α, β, γ (deg.)90.000, 107.550, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)


Mass: 45531.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylophilus ampelinus (bacteria) / Gene: praI / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A0A978C2P2

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Non-polymers , 5 types, 611 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 6% PEG 8000, 0.24 M Calcium acetate, 0.1 M Tris, Soaked with 20 mM 3,4-dihydroxybenzoate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→47.52 Å / Num. obs: 86275 / % possible obs: 100 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.031 / Net I/σ(I): 13.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4251 / CC1/2: 0.816 / Rpim(I) all: 0.319 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.0.32refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K0I

1k0i


Resolution: 1.65→47.52 Å / SU ML: 0.2086 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 21.4253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2212 4506 5.23 %
Rwork0.1818 81704 -
obs0.1838 86210 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.91 Å2
Refinement stepCycle: LAST / Resolution: 1.65→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6058 0 164 601 6823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096372
X-RAY DIFFRACTIONf_angle_d1.02838629
X-RAY DIFFRACTIONf_chiral_restr0.0661895
X-RAY DIFFRACTIONf_plane_restr0.01251137
X-RAY DIFFRACTIONf_dihedral_angle_d15.18722325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.2941460.28192711X-RAY DIFFRACTION99.93
1.67-1.690.29761590.26682689X-RAY DIFFRACTION99.96
1.69-1.710.29921440.26772742X-RAY DIFFRACTION100
1.71-1.730.30221390.26192704X-RAY DIFFRACTION100
1.73-1.760.27181610.24142736X-RAY DIFFRACTION100
1.76-1.780.29181600.23122690X-RAY DIFFRACTION100
1.78-1.810.25691350.22412686X-RAY DIFFRACTION100
1.81-1.830.25791590.21662729X-RAY DIFFRACTION99.97
1.83-1.860.22381340.20672711X-RAY DIFFRACTION99.96
1.86-1.890.26821360.20482723X-RAY DIFFRACTION99.76
1.89-1.920.29421520.22592706X-RAY DIFFRACTION99.27
1.92-1.960.2511350.20832717X-RAY DIFFRACTION99.93
1.96-20.26031480.19942724X-RAY DIFFRACTION99.86
2-2.040.22721530.19422719X-RAY DIFFRACTION99.97
2.04-2.080.26651620.20732683X-RAY DIFFRACTION99.61
2.08-2.130.23051450.18492722X-RAY DIFFRACTION100
2.13-2.180.22461720.17652670X-RAY DIFFRACTION100
2.18-2.240.24971630.18692727X-RAY DIFFRACTION99.69
2.24-2.310.2461540.18012708X-RAY DIFFRACTION99.76
2.31-2.380.20961450.17992724X-RAY DIFFRACTION99.93
2.38-2.470.23471530.17762714X-RAY DIFFRACTION99.9
2.47-2.570.20631330.17752736X-RAY DIFFRACTION100
2.57-2.680.20631470.17762743X-RAY DIFFRACTION99.97
2.68-2.830.23831420.17782727X-RAY DIFFRACTION100
2.83-30.21411600.17572737X-RAY DIFFRACTION100
3-3.240.23991550.17542732X-RAY DIFFRACTION99.9
3.24-3.560.22781390.16662760X-RAY DIFFRACTION99.93
3.56-4.080.16321660.1482729X-RAY DIFFRACTION99.97
4.08-5.130.16981540.14342777X-RAY DIFFRACTION100
5.13-47.520.17931550.17582828X-RAY DIFFRACTION99.87

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