PDB-9j2l: 4,5-DOPA-extradiol-dioxygenase from Mirabilis jalapa

ID or keywords:

Entry

Database: PDB / ID: 9j2l

Title

4,5-DOPA-extradiol-dioxygenase from Mirabilis jalapa

Components

4,5-DOPA dioxygenase extradiol

Keywords

OXIDOREDUCTASE / DOPA dioxygenase / betalamic acid / pigment

Function / homology

Function and homology information

stizolobate synthase / stizolobate synthase activity / pigment biosynthetic process / ferrous iron binding / zinc ion binding / cytoplasm
Similarity search - Function

Biological species

Mirabilis jalapa (garden four-o'clock)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.28 Å

Authors

Chou, Y.C. / Hsu, C.H.

Funding support

Taiwan, 2items

Citation

Journal: To Be Published
Title: Structure-guided design of the dopamine biocatalyst from DOPA dioxygenase
Authors: Yeh, Y.C. / Hsu, C.H.

History

Deposition	Aug 7, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 13, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9j2l.cif.gz	336.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9j2l.ent.gz	276.5 KB	Display	PDB format
PDBx/mmJSON format	9j2l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9j2l_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	9j2l_full_validation.pdf.gz	2.4 MB	Display
Data in XML	9j2l_validation.xml.gz	41.2 KB	Display
Data in CIF	9j2l_validation.cif.gz	53.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j2/9j2l ftp://data.pdbj.org/pub/pdb/validation_reports/j2/9j2l	HTTPS FTP

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Related structure data

Related structure data	8in2S S: Starting model for refinement
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
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1)

Deposited unit

A: 4,5-DOPA dioxygenase extradiol

B: 4,5-DOPA dioxygenase extradiol

C: 4,5-DOPA dioxygenase extradiol

hetero molecules

97.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 4,5-DOPA dioxygenase extradiol

hetero molecules

defined by author
Evidence: gel filtration, monomer
32.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 4,5-DOPA dioxygenase extradiol

hetero molecules

defined by author
32.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: 4,5-DOPA dioxygenase extradiol

hetero molecules

defined by author
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	142.370, 142.370, 131.628
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-406- HOH
2	1	B-442- HOH
3	1	B-481- HOH

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Protein , 1 types, 3 molecules ABC

#1: Protein	4,5-DOPA dioxygenase extradiol / MjDOD / DOPA 4 / 5-dioxygenase Mass: 31278.281 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mirabilis jalapa (garden four-o'clock) / Gene: DOD / Production host: Escherichia coli (E. coli) / References: UniProt: B6F0W8, stizolobate synthase

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Non-polymers , 6 types, 359 molecules

#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₈O₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FE2 / FE (II) ION Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.72 Å³/Da / Density % sol: 66.9 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium citrate tribasic pH6.8, 10% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97622 Å / Relative weight: 1
Reflection	Resolution: 2.28→30 Å / Num. obs: 604642 / % possible obs: 100 % / Redundancy: 9.7 % / B_iso Wilson estimate: 29.4 Å² / CC_1/2: 0.98 / R_merge(I) obs: 0.091 / Net I/av σ(I): 24.818 / Net I/σ(I): 38
Reflection shell	Resolution: 2.28→2.36 Å / Redundancy: 9.9 % / R_merge(I) obs: 0.576 / Mean I/σ(I) obs: 4.222 / Num. unique obs: 62135 / CC_1/2: 0.927 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8IN2

8in2

Resolution: 2.28→29.9 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1855	3172	3.23 %
R_work	0.1473	-	-
obs	0.1485	98192	83.22 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.28→29.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6316	0	228	323	6867

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6715
X-RAY DIFFRACTION	f_angle_d	0.938	9110
X-RAY DIFFRACTION	f_dihedral_angle_d	10.058	918
X-RAY DIFFRACTION	f_chiral_restr	0.059	934
X-RAY DIFFRACTION	f_plane_restr	0.006	1168

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 (%)
2.28-2.31	0.2546	87	0.2222	2479	X-RAY DIFFRACTION	49
2.31-2.35	0.2185	85	0.2057	2531	X-RAY DIFFRACTION	52
2.35-2.39	0.257	72	0.2044	2607	X-RAY DIFFRACTION	52
2.39-2.43	0.2248	93	0.2093	2632	X-RAY DIFFRACTION	53
2.43-2.47	0.2369	97	0.2003	2698	X-RAY DIFFRACTION	55
2.47-2.52	0.2761	85	0.1917	2866	X-RAY DIFFRACTION	58
2.52-2.57	0.1948	115	0.1709	3120	X-RAY DIFFRACTION	63
2.57-2.63	0.1941	102	0.1653	3598	X-RAY DIFFRACTION	72
2.63-2.69	0.2855	132	0.1698	4045	X-RAY DIFFRACTION	81
2.69-2.76	0.2173	158	0.1649	4448	X-RAY DIFFRACTION	90
2.76-2.83	0.2394	149	0.1504	4681	X-RAY DIFFRACTION	94
2.83-2.91	0.1979	174	0.1505	4821	X-RAY DIFFRACTION	97
2.91-3.01	0.2151	154	0.1537	4882	X-RAY DIFFRACTION	99
3.01-3.12	0.1632	169	0.149	4963	X-RAY DIFFRACTION	100
3.12-3.24	0.1918	153	0.1512	4984	X-RAY DIFFRACTION	100
3.24-3.39	0.1776	168	0.1427	4971	X-RAY DIFFRACTION	100
3.39-3.57	0.1713	183	0.1353	4929	X-RAY DIFFRACTION	100
3.57-3.79	0.1525	167	0.1276	4974	X-RAY DIFFRACTION	100
3.79-4.08	0.1539	183	0.1293	4927	X-RAY DIFFRACTION	100
4.08-4.49	0.1545	151	0.1241	4987	X-RAY DIFFRACTION	100
4.49-5.14	0.1607	157	0.1239	4956	X-RAY DIFFRACTION	100
5.14-6.46	0.1682	167	0.1555	4982	X-RAY DIFFRACTION	100
6.46-10	0.2147	171	0.1544	4939	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	0.1384	-0.09	-0.0478	0.1302	0.0262	0.152	-0.1367	0.1796	-0.0106	-0.1606	0.2665	-0.0442	0.16	-0.2048	-0.0023	0.1945	-0.0201	0.0197	0.2318	0.0331	0.1669	-2.7272	21.1848	6.4707
2	0.4342	0.0929	-0.0928	0.6515	-0.1607	0.0674	-0.1153	0.5439	-0.135	-0.5988	0.1071	-0.1034	0.2074	-0.1845	0.0082	0.233	-0.0456	0.0377	0.2858	-0.0125	0.1673	-4.3818	19.5952	-1.2851
3	0.3044	-0.1314	-0.2443	0.3875	0.1318	0.2403	0.045	-0.1993	0.3441	0.0897	-0.034	0.2812	0.0514	-0.1683	-0.0013	0.1658	-0.0232	0.0295	0.2994	-0.0173	0.2666	-11.9881	27.4498	15.6404
4	0.4468	-0.3073	-0.0028	0.3547	0.2684	0.4466	0.046	-0.0606	0.2028	0.0035	-0.0429	0.378	0.0165	-0.23	-0.008	0.1136	-0.0258	0.0174	0.2901	0.0202	0.2913	-17.4468	24.4204	12.5788
5	0.3024	0.1026	0.3885	0.1174	0.1012	0.5061	-0.0698	-0.5692	0.1777	0.1981	-0.0513	0.1302	-0.0305	-0.1671	-0.117	0.1795	-0.0098	0.102	0.3739	0.0202	0.287	-18.2384	22.5342	21.7589
6	0.9622	0.1788	-0.3301	1.1453	-0.0712	0.8229	0.0096	-0.0063	-0.0617	-0.0146	-0.0301	0.0719	0.1886	-0.1185	-0.0001	0.128	-0.0373	0.0253	0.1933	0.0273	0.1366	-6.1159	19.1099	13.6373
7	0.4375	-0.091	0.0148	0.5128	-0.1639	0.3512	0.0845	-0.1945	-0.3031	0.2124	-0.1652	-0.2253	0.304	0.1055	0.0005	0.2425	0.0089	0.029	0.2483	0.0789	0.2709	4.3033	11.2218	19.5987
8	0.2321	-0.2858	0.1104	0.385	-0.229	0.5336	-0.0179	0.0293	-0.1328	0.0899	-0.0048	-0.013	0.2773	-0.0056	0.0009	0.2516	-0.011	0.0811	0.1964	0.0167	0.2218	-1.4475	9.8176	9.6743
9	0.1651	-0.0274	-0.0679	0.1391	-0.0498	0.1397	0.0431	0.2598	0.26	-0.2412	-0.0747	-0.0394	-0.2838	0.1225	0.0006	0.2021	-0.0037	0.04	0.2306	-0.0315	0.2341	-27.0159	52.3523	16.4742
10	0.1447	-0.1426	-0.1189	0.2131	0.0416	0.2108	0.1292	0.5022	0.3558	-0.2895	-0.0115	-0.1456	-0.2903	0.1007	-0.0044	0.2463	-0.0013	0.0808	0.3062	0.0255	0.3135	-25.2167	58.26	10.9894
11	0.3191	-0.408	-0.0894	0.5688	0.0067	0.2082	-0.0296	0.0791	-0.1533	-0.0773	0.0595	-0.27	-0.0203	0.1662	0.0055	0.1301	-0.0214	0.0315	0.2475	-0.0392	0.2892	-18.0123	41.8202	20.1842
12	0.9201	-0.0419	0.1951	0.3429	-0.1256	0.9357	0.1507	0.2204	-0.0359	-0.5257	-0.0409	-0.7283	0.1782	0.3353	-0.1277	-0.2117	-0.0204	0.0202	0.3025	-0.0906	0.477	-12.5023	45.9316	19.4354
13	0.9449	-0.2589	-0.3826	1.2122	-0.0766	1.1323	0.0549	-0.044	0.0693	-0.0174	-0.0198	-0.2741	-0.0044	0.2489	0.0206	0.0984	-0.0156	0.007	0.1922	-0.047	0.2097	-21.7313	48.5054	24.2159
14	0.2573	-0.1577	-0.2413	0.1878	0.025	0.5047	0.0667	-0.1749	0.1576	0.1757	-0.008	-0.0649	-0.1572	-0.0532	0.0017	0.1337	-0.0021	-0.0033	0.1378	-0.0678	0.1883	-34.0317	52.896	32.8813
15	0.4158	-0.0662	-0.2919	0.2452	-0.0344	0.4478	0.0288	0.0453	0.2435	-0.0161	0.0136	-0.0704	-0.1701	0.0116	0.0049	0.1698	0.0083	0.0044	0.1556	-0.0461	0.267	-31.492	58.4808	24.1647
16	0.0787	-0.052	0.0214	0.0889	0.0578	0.0861	0.0819	-0.3766	-0.1149	0.3144	-0.0769	-0.067	-0.1228	0.2963	-0.0032	0.4821	-0.1731	-0.0205	0.5827	0.0829	0.3234	22.3094	23.0975	48.4252
17	0.8859	0.1782	-0.0476	0.6069	0.2893	0.1746	-0.0407	-0.6546	-0.1748	0.4576	0.1488	-0.4028	-0.1139	0.5618	-0.0496	0.5113	-0.0939	-0.1126	0.7547	0.0439	0.3032	28.1303	21.823	54.0397
18	0.3282	-0.1116	-0.1239	0.189	-0.0819	0.2257	0.292	-0.6227	0.3584	0.5538	-0.1429	0.3759	-0.5076	-0.1598	0.0016	0.6436	-0.0839	0.0707	0.5694	-0.0549	0.4245	11.0977	31.9919	50.7246
19	0.9454	-0.2216	-0.0799	0.3673	0.1413	0.5122	0.2226	-0.5191	0.397	0.7293	-0.0939	0.1989	-0.6535	0.0216	-0.0018	0.7413	-0.0867	0.1064	0.5907	-0.0629	0.3948	15.2578	34.869	51.8085
20	0.0895	-0.0683	-0.0245	0.0655	0.0194	0.0092	0.5699	-0.3856	0.3955	0.4408	-0.3183	-0.4759	-0.5724	0.4349	0.0144	0.6958	-0.2041	0.0413	0.4916	-0.0502	0.4873	24.1293	42.0962	40.8288
21	0.6385	-0.2672	0.1096	0.611	-0.6178	0.5802	0.1794	-0.376	-0.1921	0.2207	-0.1896	-0.0461	0.1069	0.1111	0.0001	0.3258	-0.0701	0.0297	0.4261	0.0228	0.3284	21.424	19.889	35.3124
22	0.1701	-0.0848	-0.0456	0.2019	-0.1635	0.2366	0.1114	-0.0923	0.2135	0.0842	-0.0323	-0.0989	-0.2158	0.2037	0.0006	0.3388	-0.0644	0.0461	0.4138	0.023	0.3109	21.0276	29.7139	31.4184
23	0.2302	-0.2185	-0.075	0.181	0.0132	0.1847	-0.0158	-0.155	0.0937	0.1352	0.0845	-0.1232	-0.1803	0.192	0.0013	0.3899	-0.1126	-0.0297	0.5334	0.0411	0.3546	28.3174	24.3872	39.7472

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 39 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 40 through 71 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 72 through 97 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 98 through 111 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 112 through 181 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 182 through 233 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 234 through 267 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 16 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 17 through 39 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 40 through 71 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 72 through 97 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 98 through 181 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 182 through 233 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 234 through 262 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1 through 16 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 17 through 39 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 40 through 71 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 72 through 139 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 140 through 156 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 157 through 196 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 197 through 233 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 234 through 262 )

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Protein , 1 types, 3 molecules ABC

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Non-polymers , 6 types, 359 molecules

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