PDB-5ce9: structure of tyrosinase from walnut (Juglans regia)

ID or keywords:

Entry

Database: PDB / ID: 5ce9

Title

structure of tyrosinase from walnut (Juglans regia)

Components

Polyphenol oxidase

Keywords

OXIDOREDUCTASE / polyphenol oxidase / tyrosinase / monophenolase activtiy / diphenolase activity

Function / homology

Function and homology information

catechol oxidase activity => GO:0004097 / pigment biosynthetic process / tyrosinase activity / metal ion binding
Similarity search - Function

Biological species

Juglans regia (English walnut)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Bijelic, A. / Pretzler, M. / Zekiri, F. / Rompel, A.

Funding support

Austria, 1items

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: The Structure of a Plant Tyrosinase from Walnut Leaves Reveals the Importance of """"Substrate-Guiding Residues"""" for Enzymatic Specificity.
Authors: Bijelic, A. / Pretzler, M. / Molitor, C. / Zekiri, F. / Rompel, A.

History

Deposition	Jul 6, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Oct 28, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 13, 2016	Group: Database references
Revision 1.2	Mar 30, 2016	Group: Data collection
Revision 1.3	Sep 6, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Feb 20, 2019	Group: Advisory / Data collection / Derived calculations Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.5	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ce9.cif.gz	394.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5ce9.ent.gz	329.9 KB	Display	PDB format
PDBx/mmJSON format	5ce9.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5ce9_validation.pdf.gz	429.7 KB	Display	wwPDB validaton report
Full document	5ce9_full_validation.pdf.gz	431.5 KB	Display
Data in XML	5ce9_validation.xml.gz	29.7 KB	Display
Data in CIF	5ce9_validation.cif.gz	44.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ce/5ce9 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/5ce9	HTTPS FTP

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Related structure data

Related structure data	2p3xS S: Starting model for refinement
Similar structure data	3msr-4 3ovg-3 3ovg-6 3ovg-4 4jb4-d 6l0j-1 6pzu-d 2ckd-d 6n31-d 6cty-1 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
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: Polyphenol oxidase

B: Polyphenol oxidase

hetero molecules

77.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	115.430, 90.940, 86.580
Angle α, β, γ (deg.)	90.00, 130.18, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Polyphenol oxidase Mass: 38410.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Juglans regia (English walnut) / References: UniProt: C0LU17
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-O / OXYGEN ATOM Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.57 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 5000 MME, ammonium sulfate, MES

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.8→44.1 Å / Num. all: 63125 / Num. obs: 88706 / % possible obs: 99.6 % / Redundancy: 6.7 % / R_merge(I) obs: 0.09833 / Net I/σ(I): 8.8
Reflection shell	R_merge(I) obs: 0.9795 / Num. measured obs: 43110 / Num. unique all: 6291

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2p3x

2p3x

Resolution: 1.8→44.098 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 22.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1875	3150	5 %
R_work	0.1697	-	-
obs	0.1706	62990	99.53 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→44.098 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5308	0	13	534	5855

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	5508
X-RAY DIFFRACTION	f_angle_d	0.989	7513
X-RAY DIFFRACTION	f_dihedral_angle_d	13.211	1965
X-RAY DIFFRACTION	f_chiral_restr	0.042	792
X-RAY DIFFRACTION	f_plane_restr	0.005	993

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 (%)
1.8-1.8281	0.3715	144	0.3545	2722	X-RAY DIFFRACTION	99
1.8281-1.8581	0.333	141	0.3251	2655	X-RAY DIFFRACTION	99
1.8581-1.8901	0.2929	143	0.3036	2722	X-RAY DIFFRACTION	99
1.8901-1.9245	0.3328	142	0.2816	2701	X-RAY DIFFRACTION	99
1.9245-1.9615	0.2642	141	0.2598	2686	X-RAY DIFFRACTION	99
1.9615-2.0016	0.2697	141	0.2485	2678	X-RAY DIFFRACTION	99
2.0016-2.0451	0.2229	142	0.2222	2712	X-RAY DIFFRACTION	100
2.0451-2.0927	0.2468	142	0.2045	2693	X-RAY DIFFRACTION	100
2.0927-2.145	0.2221	143	0.1949	2717	X-RAY DIFFRACTION	100
2.145-2.203	0.2101	144	0.192	2736	X-RAY DIFFRACTION	100
2.203-2.2678	0.2009	143	0.1838	2715	X-RAY DIFFRACTION	100
2.2678-2.341	0.1956	143	0.1756	2730	X-RAY DIFFRACTION	100
2.341-2.4247	0.1844	143	0.1697	2704	X-RAY DIFFRACTION	100
2.4247-2.5217	0.1654	144	0.1685	2727	X-RAY DIFFRACTION	99
2.5217-2.6365	0.2044	143	0.165	2715	X-RAY DIFFRACTION	100
2.6365-2.7755	0.187	144	0.1622	2741	X-RAY DIFFRACTION	100
2.7755-2.9493	0.1787	142	0.1593	2722	X-RAY DIFFRACTION	100
2.9493-3.177	0.1627	144	0.1518	2737	X-RAY DIFFRACTION	100
3.177-3.4966	0.1913	145	0.1439	2748	X-RAY DIFFRACTION	100
3.4966-4.0023	0.1436	143	0.1361	2723	X-RAY DIFFRACTION	100
4.0023-5.0413	0.1371	146	0.1286	2765	X-RAY DIFFRACTION	100
5.0413-44.1113	0.1682	147	0.1585	2791	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	1.2408	0.2087	0.3195	1.8	0.3153	1.0834	-0.0013	0.1137	0.0161	-0.1085	-0.0539	0.0597	-0.0744	0.1168	0.0609	0.2073	0.015	-0.0087	0.4748	-0.0039	0.1545	-16.7162	39.5443	2.9214
2	1.3806	1.962	-0.7472	3.1157	-0.4151	3.2446	-0.0811	-0.0034	0.2395	0.0673	0.2086	-0.2391	-0.1633	0.6683	-0.1353	0.2276	0.0021	-0.0441	0.5584	-0.0356	0.2103	-7.1277	44.4409	16.9039
3	6.5543	4.6143	2.3529	3.6336	2.216	5.9181	-0.2236	0.882	-0.2616	-0.4117	0.2721	0.1478	-0.0927	-0.095	0.017	0.2676	0.0691	-0.0532	0.6503	-0.075	0.3206	-18.6407	28.1936	-11.3457
4	0.3673	-0.0478	-0.5201	0.5033	-0.142	1.333	0.0089	0.176	-0.0765	0.0278	0.0415	-0.0761	-0.0266	0.1657	-0.0719	0.2166	0.007	-0.034	0.5589	-0.0217	0.2746	-8.5879	38.2685	9.5253
5	1.5761	0.2021	-0.3369	1.2117	0.1387	0.7557	0.0426	0.271	-0.2061	-0.07	0.0774	0.0241	0.0638	0.0605	-0.1455	0.1809	0.0341	-0.0508	0.4368	-0.0296	0.2334	-22.3573	32.0088	2.0834
6	1.5082	0.4841	1.3095	6.9476	-4.5646	4.9819	0.17	0.3041	-0.2654	-0.1454	-0.0659	-0.2874	0.4895	0.4171	-0.1066	0.3032	0.1252	-0.0753	0.4917	-0.1238	0.352	-14.3166	16.7363	-1.3184
7	4.7936	-1.941	2.0099	9.2112	-1.5091	3.1705	-0.0951	-0.2234	-0.7787	0.32	0.1136	0.1355	0.5101	0.3337	-0.0176	0.3564	0.019	-0.0377	0.435	0.0324	0.4015	-26.3929	12.8923	14.129
8	1.0672	0.1568	0.1999	1.0549	0.2135	0.9882	0.0465	-0.0103	-0.1521	0.0805	0.0297	0.0547	0.1033	0.0973	-0.0882	0.1964	0.0327	-0.0428	0.4019	0.0067	0.2316	-21.0698	31.9631	13.5776
9	5.8306	2.399	-5.1727	3.9881	-3.9403	6.2346	0.3722	-1.2953	1.1432	-0.0009	-0.0734	0.066	-0.4681	-0.0847	-0.2962	0.255	0.0226	-0.0053	0.3979	-0.1143	0.3042	-22.2586	48.4087	11.82
10	1.0069	-1.178	1.6887	5.8718	-0.8801	3.5685	0.0075	0.0311	-0.0152	-0.109	0.067	0.8084	0.0618	0.0173	-0.0654	0.1355	0.0416	-0.0124	0.4238	-0.0078	0.3081	-33.3599	32.6705	4.3366
11	4.6104	0.7208	-1.5541	3.2804	-1.2813	8.5162	-0.1648	-0.4166	-0.4101	0.381	0.0134	0.2162	0.0779	-0.9252	0.0296	0.186	-0.0088	0.027	0.5174	-0.0147	0.2929	-67.5583	40.4263	-12.9656
12	4.8921	3.0774	-4.0118	5.1394	-2.6877	5.7795	0.08	-0.2364	0.5561	0.1168	-0.005	0.0262	-0.4989	0.2061	-0.0682	0.2094	-0.0519	-0.1098	0.3428	0.0321	0.2542	-52.2536	50.4261	-15.3731
13	1.337	-1.2487	0.6521	1.1704	-0.719	5.0165	0.065	-0.133	-0.03	0.0225	-0.1146	-0.1606	0.2742	0.5498	0.0314	0.1718	0.0126	-0.0383	0.4605	-0.0136	0.3009	-36.4033	31.9331	-15.8496
14	1.8709	-0.2689	0.7522	0.9858	-0.2529	1.6419	0.0465	-0.1664	-0.1018	0.0235	0.0121	-0.0039	0.0447	-0.0167	-0.0567	0.1859	-0.0228	-0.0208	0.2929	0.0073	0.1814	-52.1928	36.3858	-15.8466
15	1.9854	-0.1829	-3.459	6.519	0.6825	6.1096	0.3117	-0.1148	-0.7019	0.1084	-0.0296	-0.0225	0.9452	-0.2423	-0.3601	0.2933	0.0174	-0.1583	0.3204	0.0441	0.4236	-49.53	17.8513	-14.7987
16	1.9985	-1.57	1.881	8.2215	-0.7683	1.9974	-0.3125	-0.3701	1.3521	1.0153	0.2786	-0.3634	-0.5039	0.9541	0.1559	0.7273	0.1317	-0.1705	0.6814	-0.013	0.6934	-52.1389	9.0608	-31.2804
17	3.9314	-2.1825	0.5635	2.3482	-0.43	1.2747	0.2458	0.4097	-0.3816	-0.2703	-0.1147	0.126	0.2602	0.0066	-0.1015	0.287	-0.0063	-0.0704	0.3613	-0.0852	0.2551	-58.1503	29.6317	-33.5346
18	3.0351	0.1958	0.2536	3.0821	-1.7034	5.157	0.1893	-0.0622	-0.3193	-0.0859	0.0329	0.0509	0.3176	-0.0477	-0.2562	0.203	-0.0151	-0.0633	0.271	-0.0114	0.2256	-53.8145	28.0458	-21.6147
19	5.131	0.3072	2.9855	1.644	0.4715	3.7268	-0.0835	0.0353	0.2397	-0.0213	-0.0181	-0.0715	-0.2481	-0.0421	0.0767	0.1961	-0.034	-0.009	0.2253	0.03	0.1858	-55.2784	47.8907	-23.8997
20	3.529	0.0722	1.1417	6.2185	0.9128	0.5308	0.0845	0.1071	-0.0503	-0.4975	0.0332	-0.3507	-0.0994	0.4803	-0.1469	0.26	0.0173	0.0414	0.509	0.006	0.1981	-41.0965	35.7011	-29.7167

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 16:54)
2	X-RAY DIFFRACTION	2	(chain A and resid 1:15)
3	X-RAY DIFFRACTION	3	(chain A and resid 55:67)
4	X-RAY DIFFRACTION	4	(chain A and resid 68:110)
5	X-RAY DIFFRACTION	5	(chain A and resid 111:154)
6	X-RAY DIFFRACTION	6	(chain A and resid 155:177)
7	X-RAY DIFFRACTION	7	(chain A and resid 178:204)
8	X-RAY DIFFRACTION	8	(chain A and resid 205:313)
9	X-RAY DIFFRACTION	9	(chain A and resid 314:319)
10	X-RAY DIFFRACTION	10	(chain A and resid 320:339)
11	X-RAY DIFFRACTION	11	(chain B and resid 1:23)
12	X-RAY DIFFRACTION	12	(chain B and resid 24:43)
13	X-RAY DIFFRACTION	13	(chain B and resid 44:64)
14	X-RAY DIFFRACTION	14	(chain B and resid 65:158)
15	X-RAY DIFFRACTION	15	(chain B and resid 159:182)
16	X-RAY DIFFRACTION	16	(chain B and resid 183:193)
17	X-RAY DIFFRACTION	17	(chain B and resid 194:238)
18	X-RAY DIFFRACTION	18	(chain B and resid 239:290)
19	X-RAY DIFFRACTION	19	(chain B and resid 291:321)
20	X-RAY DIFFRACTION	20	(chain B and resid 322:339)

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Yorodumi