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- PDB-7on9: Crystal structure of para-hydroxybenzoate-3-hydroxylase PraI -

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Basic information

Entry
Database: PDB / ID: 7on9
TitleCrystal structure of para-hydroxybenzoate-3-hydroxylase PraI
Components4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
KeywordsOXIDOREDUCTASE / P-HYDROXYBENZOATE HYDROXYLASE
Function / homology
Function and homology information


4-hydroxybenzoate 3-monooxygenase [NAD(P)H] / 4-hydroxybenzoate 3-monooxygenase [NAD(P)H] activity / 4-hydroxybenzoate 3-monooxygenase (NADH) activity / benzoate catabolic process / 4-hydroxybenzoate 3-monooxygenase (NADPH) activity / 4-hydroxybenzoate 3-monooxygenase activity / FAD binding / flavin adenine dinucleotide 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 / P-HYDROXYBENZOIC ACID / 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
Similarity search - Component
Biological speciesPaenibacillus sp. JJ-1b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsZahn, M. / McGeehan, J.E.
CitationJournal: Metab Eng / Year: 2022
Title: Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p-coumarate.
Authors: Kuatsjah, E. / Johnson, C.W. / Salvachua, D. / Werner, A.Z. / Zahn, M. / Szostkiewicz, C.J. / Singer, C.A. / Dominick, G. / Okekeogbu, I. / Haugen, S.J. / Woodworth, S.P. / Ramirez, K.J. / ...Authors: Kuatsjah, E. / Johnson, C.W. / Salvachua, D. / Werner, A.Z. / Zahn, M. / Szostkiewicz, C.J. / Singer, C.A. / Dominick, G. / Okekeogbu, I. / Haugen, S.J. / Woodworth, S.P. / Ramirez, K.J. / Giannone, R.J. / Hettich, R.L. / McGeehan, J.E. / Beckham, G.T.
History
DepositionMay 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)185,27312
Polymers181,5794
Non-polymers3,6958
Water21,1501174
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)92,6376
Polymers90,7892
Non-polymers1,8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-29 kcal/mol
Surface area30990 Å2
MethodPISA
2
B: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
C: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6376
Polymers90,7892
Non-polymers1,8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-27 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.11, 101.508, 106.849
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 45394.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. JJ-1b (bacteria) / Gene: praI / Production host: Escherichia coli (E. coli)
References: UniProt: C4TP09, 4-hydroxybenzoate 3-monooxygenase [NAD(P)H]
#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-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1174 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350 0.2 M ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.628→106.849 Å / Num. obs: 166829 / % possible obs: 95.2 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.039 / Net I/σ(I): 12.5
Reflection shellResolution: 1.628→1.731 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.853 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8343 / CC1/2: 0.49 / Rpim(I) all: 0.525 / % possible all: 62.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBE

1pbe


Resolution: 1.63→106.85 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.112
RfactorNum. reflection% reflectionSelection details
Rfree0.222 8351 -RANDOM
Rwork0.2035 ---
obs0.2044 166771 80.5 %-
Displacement parametersBiso mean: 26.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.1101 Å20 Å20 Å2
2--0.0589 Å20 Å2
3----0.169 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.63→106.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12370 0 252 1174 13796
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812962HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.917565HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4580SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2267HARMONIC5
X-RAY DIFFRACTIONt_it12962HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1618SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact12360SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion15.8
LS refinement shellResolution: 1.63→1.69 Å
RfactorNum. reflection% reflection
Rfree0.2493 157 -
Rwork0.2275 --
obs0.2286 3336 15.74 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6933-0.104-0.1060.2250.03990.6335-0.0113-0.0280.0504-0.0280.0090.02980.05040.02980.0023-0.0505-0.0118-0.0013-0.07990.0253-0.048-19.14529.2102-49.3093
20.5547-0.04740.22950.55750.04790.8438-0.01410.0093-0.00980.0093-0.0241-0.0626-0.0098-0.06260.0382-0.088-0.01520.0072-0.0737-0.0218-0.0452-55.369619.7079-46.285
30.6189-0.0878-0.21520.2737-0.01841.3785-0.04830.07050.08930.07050.0202-0.09770.0893-0.09770.0281-0.06660.01160.011-0.0709-0.0328-0.061-53.322232.2266-5.0052
41.03450.02970.17460.3191-0.02961.27480.00910.0623-0.07740.06230.0026-0.0639-0.0774-0.0639-0.0117-0.11230.0136-0.0076-0.03880.0566-0.1275-17.580121.3674-6.3004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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