PDB-3w6q: Crystal structure of melB apo-protyrosinase from Asperugillus oryzae

ID or keywords:

Entry

Database: PDB / ID: 3w6q

Title

Crystal structure of melB apo-protyrosinase from Asperugillus oryzae

Components

tyrosinase

Keywords

OXIDOREDUCTASE / Four helix bundle / METAL BINDING PROTEIN

Function / homology

Function and homology information

tyrosinase / tyrosinase activity / melanin biosynthetic process / nucleus / metal ion binding
Similarity search - Function

Biological species

Aspergillus oryzae (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.052 Å

Authors

Fujieda, N. / Yabuta, S. / Ikeda, T. / Oyama, T. / Muraki, N. / Kurisu, G. / Itoh, S.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Crystal structures of copper-depleted and copper-bound fungal pro-tyrosinase: insights into endogenous cysteine-dependent copper incorporation.
Authors: Fujieda, N. / Yabuta, S. / Ikeda, T. / Oyama, T. / Muraki, N. / Kurisu, G. / Itoh, S.

History

Deposition	Feb 20, 2013	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 19, 2013	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3w6q.cif.gz	943.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3w6q.ent.gz	786.5 KB	Display	PDB format
PDBx/mmJSON format	3w6q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3w6q_validation.pdf.gz	447.7 KB	Display	wwPDB validaton report
Full document	3w6q_full_validation.pdf.gz	458.1 KB	Display
Data in XML	3w6q_validation.xml.gz	91.2 KB	Display
Data in CIF	3w6q_validation.cif.gz	136.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/3w6q ftp://data.pdbj.org/pub/pdb/validation_reports/w6/3w6q	HTTPS FTP

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Related structure data

Related structure data	3w6wC C: citing same article (ref.)
Similar structure data	6jua-d 6ju4-d 6jud-d 6tp5-d 6juc-d 6jub-d 6b4i-2 6b4j-1 6try-d 5lqd-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: tyrosinase

B: tyrosinase

C: tyrosinase

D: tyrosinase

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

1

A: tyrosinase

B: tyrosinase

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

2

C: tyrosinase

D: tyrosinase

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

Unit cell

Length a, b, c (Å)	56.968, 108.752, 231.235
Angle α, β, γ (deg.)	90.00, 93.83, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	tyrosinase Mass: 71364.578 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: melB / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2UP46*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1820 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.87 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 20% PEG 3350, 50mM potassium Chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 7, 2011
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.05→50 Å / Num. obs: 175066 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / B_iso Wilson estimate: 20.23 Å²
Reflection shell	Resolution: 2.05→2.09 Å / % possible all: 84.7

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHENIX	(AutoSol)	model building
PHENIX	(phenix.refine: 1.8_1069)	refinement
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	(AutoSol)	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.052→39.107 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8937 / SU ML: 0.17 / σ(F): 1.35 / Phase error: 17.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1829	8543	5 %
R_work	0.1439	-	-
obs	0.1458	170928	97.33 %

Solvent computation

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

Displacement parameters

B_iso max: 85.61 Å² / B_iso mean: 25.6086 Å² / B_iso min: 2.79 Å²

Refinement step

Cycle: LAST / Resolution: 2.052→39.107 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18313	0	0	1820	20133

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	19108
X-RAY DIFFRACTION	f_angle_d	1.004	26017
X-RAY DIFFRACTION	f_dihedral_angle_d	13.056	6989
X-RAY DIFFRACTION	f_chiral_restr	0.073	2671
X-RAY DIFFRACTION	f_plane_restr	0.005	3393

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.0521-2.0754	0.211	196	0.1472	4072	74
2.0754-2.0998	0.1993	257	0.1477	4869	87
2.0998-2.1254	0.1927	250	0.1514	5032	91
2.1254-2.1523	0.2131	235	0.1466	5216	94
2.1523-2.1807	0.2111	294	0.1467	5375	96
2.1807-2.2105	0.1976	279	0.1379	5435	99
2.2105-2.2421	0.2253	257	0.1351	5572	100
2.2421-2.2756	0.1872	320	0.1318	5559	100
2.2756-2.3111	0.1793	288	0.1346	5518	100
2.3111-2.349	0.1836	295	0.1355	5541	100
2.349-2.3895	0.1973	300	0.1377	5562	100
2.3895-2.433	0.1873	283	0.1385	5474	100
2.433-2.4797	0.2017	294	0.1442	5633	100
2.4797-2.5304	0.2158	285	0.144	5501	100
2.5304-2.5854	0.1929	284	0.1485	5613	100
2.5854-2.6455	0.1976	275	0.145	5499	100
2.6455-2.7116	0.2084	286	0.1484	5624	100
2.7116-2.7849	0.1982	319	0.1483	5483	100
2.7849-2.8669	0.1777	315	0.1477	5555	100
2.8669-2.9594	0.2053	302	0.1531	5530	100
2.9594-3.0651	0.1851	295	0.1468	5545	100
3.0651-3.1878	0.1885	313	0.1484	5558	100
3.1878-3.3328	0.1892	302	0.1545	5557	100
3.3328-3.5084	0.1813	298	0.1488	5578	100
3.5084-3.728	0.1778	306	0.1491	5519	100
3.728-4.0156	0.1624	299	0.1349	5512	99
4.0156-4.4192	0.1498	269	0.1282	5471	97
4.4192-5.0575	0.1384	244	0.1258	5363	95
5.0575-6.3675	0.1721	300	0.1422	5487	97
6.3675-39.1136	0.1703	303	0.1705	5132	91

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	1.3147	0.0228	0.154	1.2065	0.1775	1.0092	-0.0404	0.0738	-0.151	-0.1692	0.049	-0.0213	0.0467	0.0805	0.0127	0.1024	-0.0051	0.0262	0.113	-0.0188	0.1072	26.3239	0.3157	69.2612
2	1.7869	-0.6451	-0.9678	1.5347	-1.2433	3.3571	-0.0681	-0.235	-0.005	0.1545	0.1244	0.0074	-0.155	0.0363	-0.0393	0.0617	-0.0341	-0.0236	0.1155	-0.0225	0.11	26.4198	10.548	83.374
3	1.1047	-0.2341	-0.0838	0.9225	0.1733	0.6585	-0.0251	-0.1326	-0.1119	0.0433	0.0259	0.0473	0.0324	0.0056	0.0025	0.0772	-0.0141	0.0111	0.1234	0.0209	0.1106	15.3543	2.1396	85.8317
4	1.306	0.1908	0.4	0.695	0.2115	2.0042	0.0354	-0.0977	-0.3761	0.0487	0.0832	-0.2487	0.2496	0.277	-0.0632	0.135	0.053	0.0012	0.1679	0.034	0.2635	33.2008	-10.8115	83.1652
5	1.0621	-0.0635	0.358	1.4063	-0.0062	1.9062	-0.0396	-0.4131	-0.2845	0.2252	0.0744	0.1081	0.1414	-0.0432	-0.0245	0.1894	0.0037	0.0397	0.3273	0.1262	0.1832	12.627	-6.7898	104.6416
6	0.8946	-0.03	0.0431	1.2129	0.1325	1.0074	-0.0597	-0.0338	0.232	-0.0743	0.0185	-0.062	-0.1497	0.0048	0.0369	0.1003	0.0064	-0.0133	0.0928	-0.0057	0.1471	-1.1531	36.7799	71.4461
7	1.0156	-0.5266	0.3145	1.2403	0.5487	3.5294	-0.0001	-0.0734	0.0069	-0.0808	0.0299	0.092	0.2	-0.2902	-0.0347	0.061	-0.0561	0.001	0.1203	0.0002	0.1475	-7.8139	22.6996	72.4081
8	0.8195	-0.1807	0.2044	0.895	-0.0622	0.6745	-0.0452	-0.1716	0.1439	0.1098	0.0297	-0.0635	-0.0618	-0.0387	0.0017	0.1032	-0.0048	-0.0156	0.162	-0.0505	0.1359	4.2843	30.4776	88.8423
9	0.9653	0.2267	-0.3625	1.5184	-0.6411	2.3993	-0.008	-0.1751	0.2973	0.0551	0.0465	0.1705	-0.2696	-0.303	-0.0636	0.13	0.0651	-0.0306	0.2202	-0.0808	0.2572	-12.2777	44.3973	83.6184
10	1.2634	0.1215	-0.0634	1.6772	0.1852	2.0113	-0.0807	-0.4431	0.2223	0.2637	0.0868	-0.0197	-0.0107	-0.0878	-0.0193	0.2174	0.0328	-0.0205	0.3828	-0.1271	0.1592	2.0268	33.5489	108.1939
11	0.842	0.1301	0.0502	1.6625	0.045	0.9388	-0.0462	0.0204	-0.1439	0.0953	0.0004	-0.0622	0.1376	-0.0101	0.0411	0.1302	-0.0151	0.0154	0.0912	0.0115	0.1269	1.2169	39.6616	40.3994
12	1.9412	0.6816	-2.296	1.5781	-1.0551	8.3559	0.0566	0.0174	0.0516	0.189	0.0191	0.2278	-0.2277	-0.1365	-0.1004	0.1117	0.0113	-0.0096	0.0703	-0.0262	0.1686	-7.1035	50.4229	37.4936
13	2.9594	-0.4635	-1.0022	2.3193	-0.1869	1.7053	-0.0441	-0.207	-0.1245	0.1514	0.0696	-0.2121	0.0621	0.1165	-0.0475	0.1526	-0.0324	-0.044	0.0992	-0.0102	0.1406	11.8411	50.5539	41.002
14	1.0512	0.4631	-0.0308	1.317	0.0142	0.6093	-0.1013	0.1915	-0.0608	-0.2995	0.0941	-0.0581	0.0741	-0.0318	0.001	0.1964	-0.0157	0.0319	0.1499	-0.0323	0.1137	7.4207	45.9695	20.1542
15	0.7042	0.3113	-0.1912	1.2172	-0.1509	1.7053	-0.0644	0.1185	-0.1294	-0.2327	0.0833	0.1969	0.2245	-0.2214	-0.0002	0.1937	-0.0621	-0.0029	0.1777	-0.0568	0.1985	-6.862	33.3145	23.4593
16	1.302	0.1799	0.0845	1.5137	0.3496	1.5383	-0.1543	0.3598	-0.1589	-0.5102	0.183	-0.1697	-0.0327	0.0042	-0.0394	0.407	-0.0672	0.0807	0.299	-0.0808	0.1579	10.2507	42.9333	4.8939
17	1.2611	0.0924	-0.0298	1.8809	0.3779	0.9783	0.0655	-0.1275	0.1212	0.2972	-0.0767	-0.076	0.0357	0.0084	0.0149	0.1616	-0.0343	-0.0188	0.1132	0.0008	0.1289	27.2142	77.0844	46.0171
18	1.7373	0.154	0.7504	1.8951	-1.3343	3.2484	0.0476	0.0245	-0.1335	0.1903	-0.0911	-0.411	0.0776	0.2701	0.065	0.1266	0.0258	-0.0345	0.0987	0.037	0.224	34.2287	66.3533	39.0142
19	1.056	0.1881	0.1467	1.4853	0.1112	0.8742	0.0761	0.0818	0.0817	-0.0741	-0.087	0.0158	-0.031	-0.0104	0.013	0.106	0.0217	0.004	0.1028	0.0174	0.1107	20.0296	74.1314	29.2258
20	1.4293	0.1551	-0.0967	1.1635	0.1769	1.7262	0.141	-0.019	0.344	-0.048	-0.0155	-0.3449	-0.21	0.2591	-0.0263	0.1513	-0.0439	0.0286	0.132	0.0636	0.3135	36.8826	87.5345	34.5295
21	1.7267	-0.0482	-0.3104	1.757	0.1085	1.7732	0.024	0.3765	0.2514	-0.4432	-0.0746	0.0473	-0.158	-0.0307	0.0212	0.3136	0.0728	0.0105	0.2861	0.1175	0.1691	19.5543	83.5092	10.3325

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq -3:140 )	A	-3 - 140
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 141:178 )	A	141 - 178
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 179:385 )	A	179 - 385
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 386:462 )	A	386 - 462
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 463:616 )	A	463 - 616
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 1:125 )	B	1 - 125
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 126:185 )	B	126 - 185
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 186:385 )	B	186 - 385
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 386:462 )	B	386 - 462
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 463:616 )	B	463 - 616
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 1:125 )	C	1 - 125
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 126:166 )	C	126 - 166
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 167:229 )	C	167 - 229
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 230:385 )	C	230 - 385
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 386:474 )	C	386 - 474
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 475:616 )	C	475 - 616
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq -3:125 )	D	-3 - 125
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 126:173 )	D	126 - 173
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 174:385 )	D	174 - 385
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 386:462 )	D	386 - 462
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 463:616 )	D	463 - 616

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