PDB-8ihg: Crystal structure of aminophenol dioxygenase from Pseudomonas spe...

ID or keywords:

Entry

Database: PDB / ID: 8ihg

Title

Crystal structure of aminophenol dioxygenase from Pseudomonas species AP-3

Components

(2-aminophenol 1,6-dioxygenase ...) x 2

Keywords

BIOSYNTHETIC PROTEIN / 2-aminophenol degradation. 2-aminophenol 1 / 6-dioxygenase

Function / homology

Function and homology information

2-aminophenol 1,6-dioxygenase / : /

dioxygenase activity /

ferrous iron binding
Similarity search - Function

Biological species

Pseudomonas sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.858 Å

Authors

Shi, Q.L. / Su, D.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of aminophenol dioxygenase from Pseudomonas species AP-3
Authors: Shi, Q.L. / Su, D.

History

Deposition	Feb 22, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Feb 28, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ihg.cif.gz	451.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8ihg.ent.gz	370.2 KB	Display	PDB format
PDBx/mmJSON format	8ihg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ih/8ihg ftp://data.pdbj.org/pub/pdb/validation_reports/ih/8ihg	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

A: 2-aminophenol 1,6-dioxygenase beta subunit

B: 2-aminophenol 1,6-dioxygenase alpha subunit

C: 2-aminophenol 1,6-dioxygenase beta subunit

D: 2-aminophenol 1,6-dioxygenase alpha subunit

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	153.475, 153.475, 312.036
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

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2-aminophenol 1,6-dioxygenase ... , 2 types, 4 molecules ACBD

#1: Protein	2-aminophenol 1,6-dioxygenase beta subunit Mass: 34483.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: amnB / Production host: Escherichia coli (E. coli) / References: UniProt: O33477, 2-aminophenol 1,6-dioxygenase
#2: Protein	2-aminophenol 1,6-dioxygenase alpha subunit Mass: 29459.303 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: amnA / Production host: Escherichia coli (E. coli) / References: UniProt: O33478

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Non-polymers , 4 types, 119 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-2AF / 2-AMINOPHENOL / 2-Aminophenol Mass: 109.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₇NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 4.06 Å³/Da / Density % sol: 69.73 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: magnesium chloride hexahydrate, 0.1 M TRIS pH 8.5, 21% v/v polyethylene glycol 8000

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 9, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.858→81.912 Å / Num. obs: 51097 / % possible obs: 100 % / Redundancy: 20 % / CC_1/2: 0.995 / Net I/σ(I): 12
Reflection shell	Resolution: 2.86→3.01 Å / Num. unique obs: 7316 / CC_1/2: 0.872

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Processing

Software

Name	Version	Classification
PHENIX	(1.15.2_3472: ???)	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.858→81.912 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2337	2000	3.92 %
R_work	0.1789	-	-
obs	0.1811	50991	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.858→81.912 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8891	0	30	113	9034

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	9178
X-RAY DIFFRACTION	f_angle_d	1.062	12479
X-RAY DIFFRACTION	f_dihedral_angle_d	3.688	6442
X-RAY DIFFRACTION	f_chiral_restr	0.058	1354
X-RAY DIFFRACTION	f_plane_restr	0.009	1624

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 (%)
2.858-2.9294	0.3616	139	0.2798	3423	X-RAY DIFFRACTION	100
2.9294-3.0087	0.3072	141	0.2514	3431	X-RAY DIFFRACTION	100
3.0087-3.0972	0.2876	139	0.2278	3426	X-RAY DIFFRACTION	100
3.0972-3.1972	0.3243	142	0.2278	3465	X-RAY DIFFRACTION	100
3.1972-3.3114	0.2998	139	0.2162	3420	X-RAY DIFFRACTION	100
3.3114-3.444	0.2861	142	0.2116	3459	X-RAY DIFFRACTION	100
3.444-3.6008	0.2591	141	0.2032	3443	X-RAY DIFFRACTION	100
3.6008-3.7906	0.2409	141	0.1776	3471	X-RAY DIFFRACTION	100
3.7906-4.0281	0.234	143	0.1621	3491	X-RAY DIFFRACTION	100
4.0281-4.3391	0.2042	142	0.1548	3491	X-RAY DIFFRACTION	100
4.3391-4.7757	0.1718	144	0.1276	3520	X-RAY DIFFRACTION	100
4.7757-5.4666	0.2051	145	0.1401	3543	X-RAY DIFFRACTION	100
5.4666-6.8868	0.2119	147	0.1764	3594	X-RAY DIFFRACTION	100
6.8868-81.912	0.1967	155	0.1721	3814	X-RAY DIFFRACTION	100

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	0.0639	0.0225	-0.1449	0.0587	-0.1535	0.1739	0.001	-0.0077	-0.0025	-0.1504	0.0831	0.1381	-0.0241	-0.3172	-0.0004	0.3298	0.0193	0.0363	0.2916	-0.0049	0.2769	49.9053	10.653	-49.3491
2	0.0974	-0.1489	-0.1963	0.1243	0.1541	0.2623	-0.0151	0.064	-0.1802	-0.2139	-0.0081	-0.1274	0.1497	-0.027	0.0029	0.3196	-0.0709	0.0725	0.2167	-0.026	0.1415	59.9506	7.1872	-62.5201
3	0.1743	-0.0744	0.2198	0.15	0.0075	0.2861	0.0453	0.0918	0.0577	-0.1942	0.0367	-0.0289	-0.0873	-0.0391	-0.0001	0.3289	-0.0622	0.0869	0.2153	-0.0111	0.2599	63.5518	12.9375	-62.1565
4	0.4344	-0.229	-0.3341	0.2624	0.4437	0.7721	0.0573	-0.0078	0.0264	-0.0902	0.0544	-0.0274	-0.2223	0.1643	0.0001	0.3939	-0.0912	0.0778	0.256	-0.0058	0.3147	61.1287	19.829	-46.118
5	0.1602	-0.1684	0.0436	0.1508	0.1387	0.1702	-0.0863	0.1339	-0.2047	0.0011	0.0817	-0.0473	0.1428	0.1358	0	0.3274	-0.0001	0.092	0.3208	-0.0586	0.3604	76.7371	-11.832	-59.5212
6	0.0127	0.003	-0.0071	0.0919	0.0601	0.056	-0.032	-0.1167	-0.1867	0.1783	0.1768	-0.1073	0.2819	-0.0806	0.0003	0.4668	0.0667	0.101	0.3824	0.032	0.2878	71.8409	-16.9078	-38.1391
7	0.1084	-0.1166	-0.246	0.3206	0.1395	0.4862	-0.0792	-0.0234	-0.0151	-0.059	0.0603	-0.0581	0.0799	0.3133	0	0.2873	-0.0206	0.059	0.3968	-0.0379	0.3552	81.4026	-8.0496	-53.3025
8	0.0574	0.0674	-0.0239	0.0891	0.0239	0.0977	0.0799	-0.0331	0.3135	0.1098	0.2672	-0.1622	-0.3773	0.4453	0.0007	0.379	-0.1399	0.0917	0.7113	-0.1142	0.5577	92.2076	-3.6845	-48.555
9	0.0791	0.2079	0.0221	0.4225	-0.0053	-0.0146	-0.085	0.2944	-0.1332	-0.3045	0.3676	-0.1626	0.12	0.3262	0.023	0.3063	0.0772	0.1174	0.7099	-0.0984	0.4952	92.212	-10.5448	-57.5748
10	0.2708	0.0269	0.3031	0.5005	0.4495	0.4781	-0.0224	-0.0508	0.0706	-0.0724	0.0416	-0.0305	-0.1687	-0.0275	0	0.1932	-0.0059	0.0305	0.1294	0.0281	0.1457	40.9038	30.9009	-20.9452
11	0.0056	0.0399	-0.0212	0.0866	-0.0496	0.0054	-0.1412	-0.0792	0.0456	-0.213	0.105	0.2723	-0.0006	-0.1111	0.0001	0.2822	0.0315	0.0241	0.2826	0.0226	0.2693	26.6723	19.5373	-16.9174
12	0.1119	-0.0416	-0.1778	0.3958	0.0469	0.6948	0.0085	0.0279	-0.0906	-0.1758	0.0213	0.0464	0.0657	-0.1187	0	0.3256	-0.0208	0.0212	0.2066	-0.0236	0.2689	40.2193	15.3808	-28.3492
13	0.0618	0.1274	0.1784	0.216	-0.0906	0.0981	0.0084	-0.0221	0.0947	0.0737	0.0649	-0.0875	-0.1253	-0.0555	-0	0.3564	0.0008	0.0122	0.2649	-0.0126	0.3126	47.686	26.7658	6.6908
14	0.0164	0.0074	-0.0163	0.0092	-0.0073	0.0162	0.1944	0.0465	-0.0089	0.0582	0.1068	-0.2373	0.0626	0.0776	-0.0001	0.2467	0.039	0.0312	0.3547	-0.0627	0.5317	67.162	18.516	-0.1259
15	0.3264	0.0789	-0.1386	0.1335	-0.1152	0.3526	-0.0135	-0.0094	-0.0093	-0.0799	0.0912	-0.0023	0.0233	0.0999	0	0.3238	0.0033	-0.0284	0.2703	-0.0101	0.3063	56.7105	20.7275	3.8704
16	0.0228	0.0438	-0.0224	0.0607	-0.0195	0.0261	0.3039	0.1704	-0.2729	0.0038	-0.0431	-0.1613	0.0115	-0.2578	0.0002	0.2885	-0.0174	-0.0561	0.2999	0.0308	0.4337	27.9666	18.7728	5.492
17	0.0091	-0.0116	0.0003	0.0066	0.0072	0.0072	0.1534	-0.0817	-0.0217	0.1211	0.2649	0.0559	0.0669	-0.1439	-0.0002	0.5117	-0.0283	0.0531	0.3784	0.0301	0.5114	36.6916	7.7181	15.2477
18	0.1869	0.1664	-0.132	0.1949	-0.142	0.2642	-0.1425	-0.0377	-0.0913	0.1284	0.1009	0.102	0.0915	-0.1741	0.0002	0.3998	0.0153	0.0227	0.2472	0.0362	0.2821	44.7115	10.0642	11.8805

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 52 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 113 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 114 through 182 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 183 through 301 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 89 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 90 through 103 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 104 through 210 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 211 through 244 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 245 through 271 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 3 through 150 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 151 through 182 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 183 through 301 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 2 through 89 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 90 through 103 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 104 through 174 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 175 through 195 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 196 through 211 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 212 through 271 )

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