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

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Basic information

Entry
Database: PDB / ID: 8jqo
TitleProtocatecuate hydroxylase from Xylophilus ampelinus complexed with imidazole
Components4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
KeywordsOXIDOREDUCTASE / p-hydroxybenzoate hydroxylase / FAD / NADPH
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / :
Function and homology information
Biological speciesXylophilus ampelinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)
C: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
D: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,91319
Polymers182,1274
Non-polymers3,78615
Water12,340685
1
A: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
D: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9229
Polymers91,0632
Non-polymers1,8597
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-31 kcal/mol
Surface area28760 Å2
MethodPISA
2
B: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)92,99110
Polymers91,0632
Non-polymers1,9288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y+1/2,-z+21
Buried area6450 Å2
ΔGint-30 kcal/mol
Surface area30570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.260, 67.389, 128.234
Angle α, β, γ (deg.)90.00, 90.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 45531.746 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 69.085 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 4% PEG 8000, 0.24 M Calcium acetate, 0.1 M Imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→46.45 Å / Num. obs: 194834 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.91 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.039 / Net I/σ(I): 10.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 9626 / CC1/2: 0.795 / Rpim(I) all: 0.311 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.0.32refinement
PHENIX1.20.1-4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K0I

1k0i


Resolution: 1.6→46.45 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 23.67 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2465 9830 5.05 %
Rwork0.2228 --
obs0.2239 194812 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11467 0 251 685 12403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511983
X-RAY DIFFRACTIONf_angle_d0.77316210
X-RAY DIFFRACTIONf_dihedral_angle_d13.994364
X-RAY DIFFRACTIONf_chiral_restr0.051688
X-RAY DIFFRACTIONf_plane_restr0.0092131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.28993260.26486072X-RAY DIFFRACTION99
1.62-1.640.28993160.26346248X-RAY DIFFRACTION99
1.64-1.660.29113470.25576077X-RAY DIFFRACTION99
1.66-1.680.27983470.25316131X-RAY DIFFRACTION99
1.68-1.70.28163430.24616144X-RAY DIFFRACTION99
1.7-1.730.27963020.25996205X-RAY DIFFRACTION99
1.73-1.750.29833270.26686142X-RAY DIFFRACTION99
1.75-1.780.31593390.27436206X-RAY DIFFRACTION99
1.78-1.810.28143060.2596143X-RAY DIFFRACTION99
1.81-1.830.29513600.26326174X-RAY DIFFRACTION99
1.83-1.870.27733540.25116134X-RAY DIFFRACTION99
1.87-1.90.272910.23936201X-RAY DIFFRACTION100
1.9-1.940.25313500.23336157X-RAY DIFFRACTION99
1.94-1.980.26283350.23516177X-RAY DIFFRACTION99
1.98-2.020.29053140.24346163X-RAY DIFFRACTION99
2.02-2.070.25393820.23526160X-RAY DIFFRACTION99
2.07-2.120.25093090.24156193X-RAY DIFFRACTION99
2.12-2.180.26633530.24356215X-RAY DIFFRACTION99
2.18-2.240.22213350.22026166X-RAY DIFFRACTION99
2.24-2.310.23483050.21586206X-RAY DIFFRACTION99
2.31-2.390.23183290.22486173X-RAY DIFFRACTION99
2.39-2.490.23933320.22216164X-RAY DIFFRACTION99
2.49-2.60.24823630.21556138X-RAY DIFFRACTION99
2.6-2.740.25842910.22266201X-RAY DIFFRACTION99
2.74-2.910.24733390.21956184X-RAY DIFFRACTION99
2.91-3.140.24433220.22286162X-RAY DIFFRACTION98
3.14-3.450.2442850.21016207X-RAY DIFFRACTION98
3.45-3.950.22883270.19986161X-RAY DIFFRACTION97
3.95-4.980.21433270.18986097X-RAY DIFFRACTION97
4.98-46.450.21422740.21466181X-RAY DIFFRACTION95

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