PDB-6dll: 2.2 Angstrom Resolution Crystal Structure of P-Hydroxybenzoate Hy...

ID or keywords:

Entry

Database: PDB / ID: 6dll

Title

2.2 Angstrom Resolution Crystal Structure of P-Hydroxybenzoate Hydroxylase from Pseudomonas putida in Complex with FAD.

Components

p-hydroxybenzoate hydroxylase

Keywords

OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / P-hydroxybenzoate Hydroxylase / FAD

Function / homology

Function and homology information

benzoate catabolic process / 4-hydroxybenzoate 3-monooxygenase / 4-hydroxybenzoate 3-monooxygenase activity / FAD binding
Similarity search - Function

Biological species

Pseudomonas putida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structural comparison of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida with PobA from other Pseudomonas spp. and other monooxygenases.
Authors: Lazar, J.T. / Shuvalova, L. / Rosas-Lemus, M. / Kiryukhina, O. / Satchell, K.J.F. / Minasov, G.

History

Deposition	Jun 1, 2018	Deposition site: RCSB / Processing site: RCSB
Supersession	Jun 13, 2018	ID: 5TTI
Revision 1.0	Jun 13, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 7, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6dll.cif.gz	667.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6dll.ent.gz	555.8 KB	Display	PDB format
PDBx/mmJSON format	6dll.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6dll_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	6dll_full_validation.pdf.gz	1.4 MB	Display
Data in XML	6dll_validation.xml.gz	68.3 KB	Display
Data in CIF	6dll_validation.cif.gz	97 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dl/6dll ftp://data.pdbj.org/pub/pdb/validation_reports/dl/6dll	HTTPS FTP

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Related structure data

Related structure data	1pbbS S: Starting model for refinement
Similar structure data	1pxb-1 1iux-1 1pbf-1 1cj4-2 1bgj-1 1iuu-1 1cj3-2 1iuv-1 1pdh-1 1pbc-1 1bkw-2 1k0j-2 1cj2-2 1bgn-1 1pbe-1 1doe-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP07306

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: p-hydroxybenzoate hydroxylase

B: p-hydroxybenzoate hydroxylase

C: p-hydroxybenzoate hydroxylase

D: p-hydroxybenzoate hydroxylase

hetero molecules

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

1

A: p-hydroxybenzoate hydroxylase

B: p-hydroxybenzoate hydroxylase

hetero molecules

defined by author&software
91 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: p-hydroxybenzoate hydroxylase

D: p-hydroxybenzoate hydroxylase

hetero molecules

defined by author&software
91 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	65.041, 152.300, 88.636
Angle α, β, γ (deg.)	90.00, 102.43, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	p-hydroxybenzoate hydroxylase Mass: 44590.676 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria) Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: pobA, PP_3537 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q88H28, 4-hydroxybenzoate 3-monooxygenase
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 895 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.7 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 13.8 mg/ml, 0.01M Tris HCl (pH 8.3), 1mM FAD; Screen: PACT (F4), 0.2M Potassium thiocyanate, 0.1M Bis-Tris propane (pH 6.5), 20% (w/v) PEG 3350.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2016 / Details: C(111)
Radiation	Monochromator: BERYLLIUM LENSES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.2→30 Å / Num. obs: 86948 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / B_iso Wilson estimate: 44.8 Å² / R_merge(I) obs: 0.059 / R_pim(I) all: 0.031 / R_rim(I) all: 0.067 / R_sym value: 0.059 / Χ²: 1.011 / Net I/σ(I): 23.8
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.805 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 4317 / CC_1/2: 0.779 / R_pim(I) all: 0.431 / R_rim(I) all: 0.915 / R_sym value: 0.805 / Χ²: 1.006 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0222	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1PBB

1pbb

Resolution: 2.2→29.61 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.942 / SU B: 11.718 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.207 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22167	4303	5.1 %	RANDOM
R_work	0.1674	-	-	-
obs	0.17013	80878	99.92 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 43.517 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.14 Å²	0 Å²	-0.74 Å²
2-	-	2.55 Å²	0 Å²
3-	-	-	-0.98 Å²

Refinement step

Cycle: 1 / Resolution: 2.2→29.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12554	0	226	895	13675

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.014	13382
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	11890
X-RAY DIFFRACTION	r_angle_refined_deg	1.284	1.679	18213
X-RAY DIFFRACTION	r_angle_other_deg	0.444	1.64	27892
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.652	5	1653
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.466	20.961	770
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.844	15	2231
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.301	15	128
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	1632
X-RAY DIFFRACTION	r_gen_planes_refined	0.04	0.02	15304
X-RAY DIFFRACTION	r_gen_planes_other	0.037	0.02	2468
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.384	2.315	6505
X-RAY DIFFRACTION	r_mcbond_other	1.384	2.315	6504
X-RAY DIFFRACTION	r_mcangle_it	2.12	3.467	8165
X-RAY DIFFRACTION	r_mcangle_other	2.12	3.467	8166
X-RAY DIFFRACTION	r_scbond_it	1.878	2.584	6877
X-RAY DIFFRACTION	r_scbond_other	1.878	2.584	6878
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.971	3.796	10039
X-RAY DIFFRACTION	r_long_range_B_refined	5.598	27.781	15482
X-RAY DIFFRACTION	r_long_range_B_other	5.571	27.71	15451
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.352	302	-
R_work	0.304	5938	-
obs	-	-	99.97 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.9194	-1.9119	0.0474	3.2949	-0.5284	0.9533	0.0889	0.1529	-0.0215	-0.1976	-0.1068	0.2036	0.0266	0.2764	0.0178	0.0574	0.0011	-0.0555	0.1199	0.025	0.1372	114.3648	-9.6676	-89.4495
2	1.3556	-0.3821	0.1033	0.7245	-0.1597	1.2809	0.0666	0.145	0.1724	0.0044	-0.0499	0.0045	-0.1725	-0.0027	-0.0167	0.1336	0.0103	-0.0683	0.0162	0.0233	0.2024	101.4291	-6.9825	-87.0496
3	3.4271	-0.5579	0.0166	0.2308	0.2973	1.3412	0.0307	-0.0094	-0.2543	0.027	-0.0092	-0.0424	0.1077	0.3167	-0.0215	0.1133	0.0198	-0.0678	0.1611	0.0537	0.2377	117.8159	-17.9412	-79.021
4	0.9718	0.0961	0.3051	3.3875	-0.4422	2.2413	0.0218	0.2113	0.0735	-0.1476	-0.1058	0.0422	0.1846	-0.1354	0.084	0.0435	0.005	-0.0171	0.0819	0.0155	0.1378	85.9817	-23.0568	-87.8584
5	0.5369	0.0035	-0.3272	0.2545	0.0533	0.8685	0.042	-0.0975	0.108	0.1004	-0.0206	-0.0052	-0.1414	0.0227	-0.0215	0.1371	0.0062	-0.0565	0.0348	0.0098	0.2437	96.9251	-11.6185	-75.2007
6	0.7363	0.3277	-0.5863	1.3277	-0.4107	1.8837	0.0063	-0.1591	0.1003	0.2471	0.0002	0.1535	-0.2864	-0.1766	-0.0066	0.2281	0.0886	-0.0226	0.1144	0.0019	0.2	64.6489	-11.9993	-41.197
7	0.7831	0.6943	-0.3828	2.3242	-0.7268	1.6309	0.0021	-0.0666	0.0584	0.2255	0.0095	0.1013	-0.2998	-0.1437	-0.0116	0.1407	0.0827	-0.0164	0.0618	0.0044	0.1318	66.5562	-12.8231	-43.2375
8	2.0793	0.6748	-0.0533	2.3209	-1.4105	2.9061	-0.1341	-0.0396	-0.3432	0.0555	0.0277	0.1503	0.2299	-0.3556	0.1063	0.2045	0.0248	0.019	0.126	0.0071	0.2631	59.6372	-30.9959	-42.9651
9	2.6213	0.2456	0.9412	1.2087	0.4459	3.1928	0.1792	-0.393	0.0572	0.5759	-0.1129	-0.3164	-0.0734	0.394	-0.0663	0.3304	-0.0807	-0.1374	0.2738	0.0414	0.188	89.5754	-12.1186	-40.1048
10	1.0747	0.2012	-0.5585	0.8177	-0.1519	1.1817	0.0055	-0.0337	0.0046	0.0833	0.0154	0.0078	-0.1029	-0.0033	-0.0209	0.1276	0.0299	-0.0611	0.0238	0.022	0.1236	74.6217	-15.5541	-54.1305
11	2.6574	-0.8605	1.3468	2.1365	0.3571	3.7441	0.2675	-0.1421	0.0145	0.4659	-0.108	0.0089	0.5132	0.2358	-0.1595	0.4915	0.041	-0.0461	0.1011	-0.01	0.1252	93.045	-46.2385	-9.0869
12	1.664	0.9532	1.2588	1.867	1.7873	2.7468	0.1781	0.0082	-0.0456	0.6498	-0.0071	-0.0348	0.7449	0.2001	-0.171	0.5222	0.0487	-0.0443	0.0575	0.0162	0.1734	87.7178	-53.3759	-18.1343
13	1.7237	-0.3875	0.8017	2.6003	1.9799	4.1856	0.0277	0.2227	0.3384	0.207	-0.0238	-0.106	0.1165	0.8695	-0.0039	0.3143	0.0097	-0.0563	0.3147	-0.0073	0.2017	98.8825	-36.2733	-13.1372
14	1.0919	-0.1874	0.3155	1.1995	0.2325	2.0012	0.0134	0.064	-0.1388	0.3228	0.0755	0.0679	0.1851	0.1534	-0.0889	0.3017	0.0569	0.0142	0.0285	0.0233	0.1397	81.7445	-47.2753	-27.6422
15	0.2249	0.2303	-0.3079	0.7858	0.8813	3.1556	0.0116	0.0015	-0.0827	0.1786	0.1803	-0.1874	0.2749	0.5217	-0.1919	0.2761	0.0987	-0.0472	0.2139	-0.0513	0.2095	91.0457	-51.7954	-38.1772
16	1.3895	-0.5247	0.0076	2.1917	-0.2468	1.1116	-0.0383	0.0212	-0.2008	-0.6451	0.06	-0.2682	0.3382	0.1107	-0.0217	0.4599	-0.04	0.1035	0.0466	-0.0726	0.2263	91.3261	-58.3781	-76.4561
17	1.5428	-0.0691	0.3384	2.9125	-2.6031	2.4188	-0.1683	0.0272	0.0745	-0.6002	0.1154	0.01	0.3623	-0.1047	0.053	0.6746	-0.0557	-0.0715	0.102	-0.0715	0.1876	78.8825	-44.4801	-82.7981
18	3.403	0.0766	-1.3011	2.4336	0.7087	2.2793	0.1311	-0.0243	0.1772	-0.1989	0.0479	-0.7145	-0.0956	0.4896	-0.179	0.1766	-0.0368	0.0606	0.2512	-0.0701	0.3051	105.0721	-48.4412	-63.0931
19	1.5544	0.2812	0.5182	1.7306	0.4581	1.3773	0.0157	0.0957	-0.1217	-0.2822	0.1258	-0.4009	0.0244	0.2648	-0.1415	0.2212	-0.0455	0.0564	0.0726	-0.0656	0.1989	95.1292	-50.7869	-68.0193
20	0.2851	-0.2332	0.2517	1.2661	0.9032	2.6037	0.0065	-0.1045	-0.1563	-0.0158	0.0773	-0.0716	0.232	0.0277	-0.0837	0.2663	-0.0131	-0.0093	0.1305	0.0282	0.2483	88.5476	-54.1101	-55.4531

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 45
2	X-RAY DIFFRACTION	2	A	46 - 141
3	X-RAY DIFFRACTION	3	A	142 - 179
4	X-RAY DIFFRACTION	4	A	180 - 246
5	X-RAY DIFFRACTION	5	A	247 - 395
6	X-RAY DIFFRACTION	6	B	-2 - 81
7	X-RAY DIFFRACTION	7	B	82 - 137
8	X-RAY DIFFRACTION	8	B	138 - 175
9	X-RAY DIFFRACTION	9	B	176 - 254
10	X-RAY DIFFRACTION	10	B	255 - 395
11	X-RAY DIFFRACTION	11	C	-1 - 44
12	X-RAY DIFFRACTION	12	C	45 - 145
13	X-RAY DIFFRACTION	13	C	146 - 171
14	X-RAY DIFFRACTION	14	C	172 - 321
15	X-RAY DIFFRACTION	15	C	322 - 395
16	X-RAY DIFFRACTION	16	D	-1 - 137
17	X-RAY DIFFRACTION	17	D	138 - 175
18	X-RAY DIFFRACTION	18	D	176 - 231
19	X-RAY DIFFRACTION	19	D	232 - 318
20	X-RAY DIFFRACTION	20	D	319 - 395

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Yorodumi