PDB-8weq: p-hydroxybenzoate 3-monooxygenase

ID or keywords:

Entry

Database: PDB / ID: 8weq

Title

p-hydroxybenzoate 3-monooxygenase

Components

4-hydroxybenzoate 3-monooxygenase

Keywords

OXIDOREDUCTASE / 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 species

Arthrobacter sp. PAMC25564 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.29 Å

Authors

Kim, S.B. / Park, H.H.

Funding support

Korea, Republic Of, 1items

Citation

Journal: To Be Published
Title: Structure of p-hydroxybenzoate 3-monooxygenase
Authors: Kim, S.B. / Park, H.H.

History

Deposition	Sep 18, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 18, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8weq.cif.gz	318.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8weq.ent.gz	256.2 KB	Display	PDB format
PDBx/mmJSON format	8weq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8weq_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8weq_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8weq_validation.xml.gz	66.2 KB	Display
Data in CIF	8weq_validation.cif.gz	86.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/we/8weq ftp://data.pdbj.org/pub/pdb/validation_reports/we/8weq	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

C: 4-hydroxybenzoate 3-monooxygenase

A: 4-hydroxybenzoate 3-monooxygenase

B: 4-hydroxybenzoate 3-monooxygenase

D: 4-hydroxybenzoate 3-monooxygenase

hetero molecules

179 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: light scattering

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 number	4
Space group name H-M	P12₁1

#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 interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.25 Å³/Da / Density % sol: 62.16 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 125 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97942 Å / Relative weight: 1
Reflection	Resolution: 3.29→29.901 Å / Num. obs: 33249 / % possible obs: 96.94 % / Redundancy: 6.8 % / CC_1/2: 0.997 / Net I/σ(I): 14.19
Reflection shell	Resolution: 3.29→3.408 Å / Num. unique obs: 3361 / CC_1/2: 0.861

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.29→29.901 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.878 / Cross valid method: FREE R-VALUE / ESU R Free: 0.546
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2558	1663	5.002 %
R_work	0.1955	31586	-
all	0.199	-	-
obs	-	33249	96.942 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 75.42 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.163 Å²	0 Å²	0.685 Å²
2-	-	-2.78 Å²	-0 Å²
3-	-	-	-2.061 Å²

Refinement step

Cycle: LAST / Resolution: 3.29→29.901 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12444	0	159	0	12603

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.013	12926
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	11674
X-RAY DIFFRACTION	r_angle_refined_deg	1.908	1.636	17555
X-RAY DIFFRACTION	r_angle_other_deg	2.374	1.583	26763
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.198	5	1572
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.03	21.295	772
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.65	15	2008
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.243	15	112
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	1607
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	14938
X-RAY DIFFRACTION	r_gen_planes_other	0.015	0.02	3249
X-RAY DIFFRACTION	r_nbd_refined	0.243	0.2	3354
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.271	0.2	12774
X-RAY DIFFRACTION	r_nbtor_refined	0.205	0.2	6386
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	6962
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.215	0.2	249
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.125	0.2	20
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.181	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.375	0.2	62
X-RAY DIFFRACTION	r_mcbond_it	3.936	8.1	6300
X-RAY DIFFRACTION	r_mcbond_other	3.933	8.099	6299
X-RAY DIFFRACTION	r_mcangle_it	5.891	12.138	7868
X-RAY DIFFRACTION	r_mcangle_other	5.893	12.139	7869
X-RAY DIFFRACTION	r_scbond_it	5.423	8.219	6626
X-RAY DIFFRACTION	r_scbond_other	5.423	8.22	6627
X-RAY DIFFRACTION	r_scangle_it	7.615	12.252	9687
X-RAY DIFFRACTION	r_scangle_other	7.615	12.252	9688
X-RAY DIFFRACTION	r_lrange_it	8.211	93.616	15070
X-RAY DIFFRACTION	r_lrange_other	8.212	93.622	15071

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.29-3.375	0.336	126	0.272	2391	X-RAY DIFFRACTION	98.5513
3.375-3.468	0.321	120	0.253	2288	X-RAY DIFFRACTION	98.0855
3.468-3.568	0.319	117	0.236	2208	X-RAY DIFFRACTION	97.5661
3.568-3.678	0.264	114	0.21	2172	X-RAY DIFFRACTION	99.0897
3.678-3.798	0.311	111	0.213	2112	X-RAY DIFFRACTION	98.4936
3.798-3.931	0.26	107	0.193	2037	X-RAY DIFFRACTION	98.2135
3.931-4.079	0.238	101	0.189	1917	X-RAY DIFFRACTION	94.9647
4.079-4.245	0.25	96	0.178	1820	X-RAY DIFFRACTION	93.6919
4.245-4.434	0.219	96	0.166	1819	X-RAY DIFFRACTION	98.9153
4.434-4.65	0.204	90	0.16	1717	X-RAY DIFFRACTION	98.5278
4.65-4.9	0.239	87	0.152	1654	X-RAY DIFFRACTION	98.7521
4.9-5.197	0.231	83	0.166	1574	X-RAY DIFFRACTION	98.0473
5.197-5.554	0.241	77	0.197	1465	X-RAY DIFFRACTION	97.967
5.554-5.997	0.331	70	0.22	1331	X-RAY DIFFRACTION	94.9187
5.997-6.567	0.287	62	0.221	1183	X-RAY DIFFRACTION	92.5651
6.567-7.337	0.242	61	0.213	1154	X-RAY DIFFRACTION	98.1422
7.337-8.462	0.203	52	0.191	996	X-RAY DIFFRACTION	97.4884
8.462-10.34	0.201	45	0.18	837	X-RAY DIFFRACTION	95.558
10.34-14.526	0.209	31	0.187	601	X-RAY DIFFRACTION	88.2682
14.526-29.901	0.44	17	0.237	311	X-RAY DIFFRACTION	78.0952

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