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- PDB-8weq: p-hydroxybenzoate 3-monooxygenase -

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Basic information

Entry
Database: PDB / ID: 8weq
Titlep-hydroxybenzoate 3-monooxygenase
Components4-hydroxybenzoate 3-monooxygenase
KeywordsOXIDOREDUCTASE / hydroxylase / FAD binding Flavoprotein / Metabolic engineering / Monooxygenase
Function / homology: / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / FAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / 4-hydroxybenzoate 3-monooxygenase
Function and homology information
Biological speciesArthrobacter sp. PAMC25564 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsKim, S.B. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Structure of p-hydroxybenzoate 3-monooxygenase
Authors: Kim, S.B. / Park, H.H.
History
DepositionSep 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 4-hydroxybenzoate 3-monooxygenase
A: 4-hydroxybenzoate 3-monooxygenase
B: 4-hydroxybenzoate 3-monooxygenase
D: 4-hydroxybenzoate 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,2377
Polymers176,8804
Non-polymers2,3573
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.740, 178.030, 89.130
Angle α, β, γ (deg.)90.000, 116.167, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4-hydroxybenzoate 3-monooxygenase / p-hydroxybenzoate 3-monooxygenase


Mass: 44220.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. PAMC25564 (bacteria) / Gene: E5206_03645 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P7SP66
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
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: 3.25 Å3/Da / Density % sol: 62.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Magnesium chloride hexahydrate, 10% (v/v) Ethylene glycol, 0.1M HEPES pH 7.5, 15% (v/v) PEG Smear Medium, 5% (v/v) 2-Propanol

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 3.29→29.901 Å / Num. obs: 33249 / % possible obs: 96.94 % / Redundancy: 6.8 % / CC1/2: 0.997 / Net I/σ(I): 14.19
Reflection shellResolution: 3.29→3.408 Å / Num. unique obs: 3361 / CC1/2: 0.861

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.29→29.901 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: FREE R-VALUE / ESU R Free: 0.546
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2558 1663 5.002 %
Rwork0.1955 31586 -
all0.199 --
obs-33249 96.942 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 75.42 Å2
Baniso -1Baniso -2Baniso -3
1-5.163 Å20 Å20.685 Å2
2---2.78 Å2-0 Å2
3----2.061 Å2
Refinement stepCycle: LAST / Resolution: 3.29→29.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12444 0 159 0 12603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01312926
X-RAY DIFFRACTIONr_bond_other_d0.0360.01711674
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.63617555
X-RAY DIFFRACTIONr_angle_other_deg2.3741.58326763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19851572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.0321.295772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65152008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.24315112
X-RAY DIFFRACTIONr_chiral_restr0.1020.21607
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214938
X-RAY DIFFRACTIONr_gen_planes_other0.0150.023249
X-RAY DIFFRACTIONr_nbd_refined0.2430.23354
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2710.212774
X-RAY DIFFRACTIONr_nbtor_refined0.2050.26386
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.26962
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1250.220
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.214
X-RAY DIFFRACTIONr_nbd_other0.3750.262
X-RAY DIFFRACTIONr_mcbond_it3.9368.16300
X-RAY DIFFRACTIONr_mcbond_other3.9338.0996299
X-RAY DIFFRACTIONr_mcangle_it5.89112.1387868
X-RAY DIFFRACTIONr_mcangle_other5.89312.1397869
X-RAY DIFFRACTIONr_scbond_it5.4238.2196626
X-RAY DIFFRACTIONr_scbond_other5.4238.226627
X-RAY DIFFRACTIONr_scangle_it7.61512.2529687
X-RAY DIFFRACTIONr_scangle_other7.61512.2529688
X-RAY DIFFRACTIONr_lrange_it8.21193.61615070
X-RAY DIFFRACTIONr_lrange_other8.21293.62215071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.3750.3361260.2722391X-RAY DIFFRACTION98.5513
3.375-3.4680.3211200.2532288X-RAY DIFFRACTION98.0855
3.468-3.5680.3191170.2362208X-RAY DIFFRACTION97.5661
3.568-3.6780.2641140.212172X-RAY DIFFRACTION99.0897
3.678-3.7980.3111110.2132112X-RAY DIFFRACTION98.4936
3.798-3.9310.261070.1932037X-RAY DIFFRACTION98.2135
3.931-4.0790.2381010.1891917X-RAY DIFFRACTION94.9647
4.079-4.2450.25960.1781820X-RAY DIFFRACTION93.6919
4.245-4.4340.219960.1661819X-RAY DIFFRACTION98.9153
4.434-4.650.204900.161717X-RAY DIFFRACTION98.5278
4.65-4.90.239870.1521654X-RAY DIFFRACTION98.7521
4.9-5.1970.231830.1661574X-RAY DIFFRACTION98.0473
5.197-5.5540.241770.1971465X-RAY DIFFRACTION97.967
5.554-5.9970.331700.221331X-RAY DIFFRACTION94.9187
5.997-6.5670.287620.2211183X-RAY DIFFRACTION92.5651
6.567-7.3370.242610.2131154X-RAY DIFFRACTION98.1422
7.337-8.4620.203520.191996X-RAY DIFFRACTION97.4884
8.462-10.340.201450.18837X-RAY DIFFRACTION95.558
10.34-14.5260.209310.187601X-RAY DIFFRACTION88.2682
14.526-29.9010.44170.237311X-RAY DIFFRACTION78.0952

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