PDB-4z0y: Active aurone synthase (polyphenol oxidase), copper B : sulfohist...

ID or keywords:

Entry

Database: PDB / ID: 4z0y

Title

Active aurone synthase (polyphenol oxidase), copper B : sulfohistidine ~ 1.4 : 1

Components

(Aurone synthase) x 2

Keywords

OXIDOREDUCTASE / Polyphenol oxidase / Aurone synthase / Type III copper protein

Function / homology

Function and homology information

pigment biosynthetic process / catechol oxidase activity / metal ion binding
Similarity search - Function

Biological species

Coreopsis grandiflora (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Molitor, C. / Mauracher, S.G. / Rompel, A.

Funding support

Austria, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Aurone synthase is a catechol oxidase with hydroxylase activity and provides insights into the mechanism of plant polyphenol oxidases.
Authors: Molitor, C. / Mauracher, S.G. / Rompel, A.

History

Deposition	Mar 26, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Apr 6, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 13, 2016	Group: Database references
Revision 1.2	Mar 7, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Nov 21, 2018	Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.4	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 / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4z0y.cif.gz	838.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4z0y.ent.gz	704.5 KB	Display	PDB format
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Validation report

Summary document	4z0y_validation.pdf.gz	491.3 KB	Display	wwPDB validaton report
Full document	4z0y_full_validation.pdf.gz	495.6 KB	Display
Data in XML	4z0y_validation.xml.gz	72.5 KB	Display
Data in CIF	4z0y_validation.cif.gz	112 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z0/4z0y ftp://data.pdbj.org/pub/pdb/validation_reports/z0/4z0y	HTTPS FTP

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Related structure data

Related structure data	4z0zC 4z11C 4z12C 4z13C 1bt3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4z10-1 4z10-3 4z0z-1 4z0z-3 6ogm-d 4z0z-2 6uqz-d 6uqw-d 4p87-d 1t8l-d Search similar-shape structures by Omokage search (details) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Aurone synthase

E: Aurone synthase

B: Aurone synthase

F: Aurone synthase

C: Aurone synthase

G: Aurone synthase

D: Aurone synthase

H: Aurone synthase

hetero molecules

168 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: Aurone synthase

G: Aurone synthase

hetero molecules

A: Aurone synthase

E: Aurone synthase

hetero molecules

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

2

A: Aurone synthase

E: Aurone synthase

hetero molecules

C: Aurone synthase

G: Aurone synthase

hetero molecules

defined by author&software
83.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: Aurone synthase

F: Aurone synthase

D: Aurone synthase

H: Aurone synthase

hetero molecules

defined by author&software
83.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	88.720, 90.560, 182.590
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Aurone synthase Mass: 40169.785 Da / Num. of mol.: 4 / Fragment: UNP residues 86-435 / Source method: isolated from a natural source / Source: (natural) Coreopsis grandiflora (plant) / Tissue: petals / References: UniProt: A0A075DN54
#2: Protein/peptide	Aurone synthase Mass: 1528.596 Da / Num. of mol.: 4 / Fragment: UNP residues 523-537 / Source method: isolated from a natural source Details: C-terminal fragment. Cleaved from activated protein but attached via disulphide bond. Source: (natural) Coreopsis grandiflora (plant) / Tissue: petals / References: UniProt: A0A075DN54
#3: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2067 / 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: 2.23 Å³/Da / Density % sol: 44.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 23-25 % PEG-4000, 500 mM sodium chloride, 100 mM sodium formiate, 50 mM sodium citrate, pH 6.4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 20, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.23953 Å / Relative weight: 1
Reflection	Resolution: 1.6→45.65 Å / Num. obs: 192559 / % possible obs: 99.4 % / Redundancy: 6.34 % / R_merge(I) obs: 0.108 / Net I/σ(I): 11.3
Reflection shell	Resolution: 1.6→1.66 Å / Redundancy: 4.51 % / Mean I/σ(I) obs: 1.8 / % possible all: 96.14

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
XSCALE		data scaling
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1bt3

1bt3

Resolution: 1.6→45.648 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1938	9621	5 %	Random selection
R_work	0.1569	-	-	-
obs	0.1587	192430	99.33 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→45.648 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11429	0	38	2067	13534

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	11954
X-RAY DIFFRACTION	f_angle_d	1.138	16264
X-RAY DIFFRACTION	f_dihedral_angle_d	12.302	4282
X-RAY DIFFRACTION	f_chiral_restr	0.045	1649
X-RAY DIFFRACTION	f_plane_restr	0.006	2169

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 (%)
1.6-1.6182	0.3143	297	0.2927	5646	X-RAY DIFFRACTION	93
1.6182-1.6372	0.3144	310	0.2883	5886	X-RAY DIFFRACTION	97
1.6372-1.6572	0.306	314	0.2675	5952	X-RAY DIFFRACTION	98
1.6572-1.6782	0.2741	319	0.2482	6061	X-RAY DIFFRACTION	99
1.6782-1.7003	0.2793	317	0.2366	6033	X-RAY DIFFRACTION	100
1.7003-1.7235	0.2689	319	0.222	6048	X-RAY DIFFRACTION	100
1.7235-1.7482	0.2491	317	0.2119	6062	X-RAY DIFFRACTION	100
1.7482-1.7743	0.2436	322	0.2	6097	X-RAY DIFFRACTION	100
1.7743-1.802	0.2225	317	0.1924	6037	X-RAY DIFFRACTION	100
1.802-1.8315	0.2363	319	0.1873	6048	X-RAY DIFFRACTION	99
1.8315-1.8631	0.2106	321	0.1747	6093	X-RAY DIFFRACTION	100
1.8631-1.897	0.2192	319	0.176	6068	X-RAY DIFFRACTION	100
1.897-1.9335	0.2234	320	0.1678	6085	X-RAY DIFFRACTION	100
1.9335-1.973	0.1886	321	0.1616	6092	X-RAY DIFFRACTION	100
1.973-2.0159	0.1956	321	0.1597	6100	X-RAY DIFFRACTION	100
2.0159-2.0627	0.2067	318	0.1559	6062	X-RAY DIFFRACTION	100
2.0627-2.1143	0.1819	322	0.144	6115	X-RAY DIFFRACTION	100
2.1143-2.1715	0.1865	319	0.1411	6067	X-RAY DIFFRACTION	100
2.1715-2.2354	0.1898	322	0.1423	6114	X-RAY DIFFRACTION	100
2.2354-2.3075	0.1789	323	0.1369	6115	X-RAY DIFFRACTION	100
2.3075-2.39	0.191	321	0.1378	6109	X-RAY DIFFRACTION	100
2.39-2.4857	0.1751	322	0.1369	6105	X-RAY DIFFRACTION	100
2.4857-2.5988	0.1792	323	0.1334	6146	X-RAY DIFFRACTION	100
2.5988-2.7358	0.1897	323	0.136	6129	X-RAY DIFFRACTION	100
2.7358-2.9072	0.1692	324	0.1348	6150	X-RAY DIFFRACTION	100
2.9072-3.1316	0.161	325	0.1347	6192	X-RAY DIFFRACTION	100
3.1316-3.4467	0.1881	326	0.1347	6189	X-RAY DIFFRACTION	100
3.4467-3.9452	0.1541	328	0.1351	6229	X-RAY DIFFRACTION	100
3.9452-4.9695	0.1601	331	0.1314	6288	X-RAY DIFFRACTION	100
4.9695-45.6661	0.1967	341	0.1779	6491	X-RAY DIFFRACTION	99

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	0.3738	-0.0458	0.0527	0.1989	0.0416	0.7802	-0.0122	0.0316	-0.0392	0.0369	0.0386	-0.02	-0.0461	-0.0291	0.0233	0.1306	0.0611	-0.0202	0.1335	-0.005	0.1211	4.7437	102.9922	211.263
2	0.3614	-0.097	0.2043	0.36	0.073	0.1597	-0.1	-0.1035	0.0882	0.0301	0.0412	0.011	-0.1281	-0.1156	-0.0266	0.1331	0.0782	-0.0079	0.1824	-0.0066	0.124	-6.5687	109.1853	217.5483
3	0.4141	-0.0239	0.1613	0.0869	0.018	0.0725	-0.1845	-0.3495	0.0759	0.2135	0.1129	0.1261	-0.0709	-0.187	-0.1193	0.2575	0.1704	0.0352	0.3483	0.0071	0.1242	-9.0662	105.9725	236.6708
4	0.054	-0.0519	0.0465	0.0461	-0.0296	0.0728	-0.1178	-0.2018	-0.098	0.2135	0.0235	-0.0174	-0.0946	0.0325	-0.0003	0.2006	0.0654	-0.0355	0.1811	-0.0157	0.1873	13.1922	103.0844	231.3087
5	0.0802	-0.0665	-0.0252	0.0564	0.0082	0.0222	-0.0068	-0.0861	-0.0109	0.1479	-0.0098	0.0235	0.1341	-0.074	0	0.1887	0.0494	-0.0014	0.1762	0.0095	0.1457	-2.7833	97.8439	224.3954
6	0.468	-0.1021	0.2679	0.5331	0.2297	0.296	-0.0825	-0.0429	0.0835	0.0106	0.0411	-0.0798	-0.24	-0.1058	-0.1138	0.1514	0.0742	-0.0395	0.1403	-0.0148	0.1245	8.3701	111.9597	221.5111
7	0.0709	-0.0118	0.0453	0.2074	0.0057	0.0437	-0.0495	-0.0107	0.0824	-0.049	-0.0808	-0.1356	-0.2461	-0.0325	-0.0263	0.2287	0.0498	-0.0493	0.1578	-0.018	0.18	9.0589	117.4521	217.088
8	0.3588	0.0095	-0.2284	0.3816	-0.5523	1.0924	0.0141	-0.0415	-0.0252	-0.0118	-0.005	0.0031	0.0011	0.0309	0.0141	0.0981	-0.0238	-0.0009	0.0994	0.0125	0.1029	43.2775	84.1729	246.5779
9	0.0793	0.0635	-0.1082	0.2304	-0.2449	0.2668	0.0292	-0.0102	-0.0144	0.0536	0.0578	0.0336	0.0343	-0.1133	0.0161	0.1073	-0.0276	-0.0084	0.1179	0.0252	0.1143	35.7247	83.588	240.8149
10	0.1423	0.0736	-0.1536	0.3467	-0.4334	0.5507	-0.0357	-0.0093	0.0015	-0.0704	-0.0826	-0.1139	0.0734	0.2209	-0.0251	0.104	0.0213	0.013	0.1391	0.0438	0.1285	56.2691	87.178	229.8438
11	0.3776	0.0466	-0.2636	0.4914	0.0805	0.2135	-0.0464	0.1478	-0.1572	-0.105	0.1191	-0.0533	0.1861	-0.2805	0.0952	0.1508	-0.0818	-0.0392	0.1919	0.0283	0.1503	32.4753	82.3777	224.8378
12	0.2389	0.0808	-0.2995	0.422	-0.5305	0.6486	-0.0283	0.0319	0.0211	-0.1091	0.0179	-0.0076	0.1798	-0.086	-0.0358	0.1124	-0.0072	0.0011	0.1068	0.0198	0.1072	41.8813	85.3261	233.5803
13	0.0327	0.0015	0.044	0.0647	0.0066	0.105	0.0339	0.0322	0.0432	0.0222	0.0246	0.0473	-0.2031	-0.1038	0.0007	0.1264	0.0166	0.0149	0.1311	0.0328	0.1493	36.0187	96.8028	239.0605
14	0.2799	-0.1727	0.1394	0.3857	-0.0842	0.7397	0.0063	0.0361	-0.0073	-0.076	0.0029	-0.0033	0.1338	0.0313	0.0065	0.1051	0.0312	0.0073	0.0992	0.0056	0.099	-0.006	80.8347	180.9984
15	0.4607	-0.1555	0.0603	0.3865	0.0222	0.6408	-0.0145	-0.0385	-0.0354	0.0501	0.0338	-0.0098	0.1847	0.0089	0.0233	0.1175	0.0413	0.0009	0.093	0.0103	0.1055	1.1302	78.4716	194.445
16	0.1126	0.0338	-0.1014	0.0129	-0.0283	0.0904	0.0008	0.0206	-0.0676	0.1077	-0.0277	0.0697	0.2062	-0.0769	-0.017	0.2149	0.0041	0.0041	0.1101	0.0049	0.1755	-9.4861	69.2558	187.6475
17	0.0976	-0.0874	0.0161	0.1987	-0.1122	0.0706	-0.0363	0.0689	0.0598	-0.0439	0.0479	-0.0059	0.0059	-0.0254	-0	0.098	-0.0013	-0.0042	0.1273	0.0097	0.1223	40.424	117.4503	182.0118
18	0.4187	-0.1569	0.1227	0.2836	-0.184	0.2601	0.0036	0.0665	-0.0338	-0.0978	0.0004	0.0136	0.1232	-0.0124	0.0001	0.1067	0.0022	0.0023	0.0883	-0.0057	0.1019	42.3605	102.4314	183.2887
19	0.3259	-0.0102	-0.1541	0.1657	-0.1466	0.204	-0.0595	-0.01	-0.0915	-0.0273	0.0282	-0.0735	0.1679	0.0577	-0.0004	0.133	0.0219	0.021	0.1131	-0.0048	0.1394	57.1871	97.8911	190.3009
20	0.0043	0.0153	-0.0168	0.1	-0.1552	0.2778	-0.0737	-0.1233	0.0175	0.0205	0.0487	-0.016	0.0461	-0.031	0	0.1193	0.0233	0.0076	0.1154	0.0063	0.1313	45.909	103.2929	205.4463
21	0.1019	-0.0627	-0.015	0.1061	0.0549	0.0295	-0.0302	-0.0305	-0.0386	0.0474	0.0402	-0.0541	0.0413	-0.0102	0.009	0.0952	0.0196	-0.0022	0.0975	-0.0018	0.1174	50.6019	110.0008	195.8297
22	0.1464	-0.1315	0.0295	0.2884	0.0119	0.1623	-0.0112	0.0479	-0.1463	-0.0024	0.0135	0.0711	0.152	-0.021	-0.0001	0.1122	-0.0074	-0.0015	0.0993	0.0106	0.1262	36.4879	98.9824	192.2031
23	0.0211	0.0428	0.0127	0.0828	0.0381	0.0676	-0.0344	-0.009	-0.1176	0.0117	0.0862	0.108	0.1023	-0.0247	0	0.1451	-0.0091	-0.0011	0.0936	0.0011	0.1569	34.4977	94.2202	187.3605
24	0.0064	0.0059	0.0169	0.0595	0.0454	0.0589	0.0556	-0.0221	-0.018	-0.0206	-0.1763	-0.1155	-0.0027	-0.0226	-0.1154	0.3556	0.1644	0.0495	0.6889	0.1715	0.2487	-6.1224	106.2807	247.3248
25	0.0104	0.0113	0.0059	0.0124	0.0054	0.0102	-0.0275	0.1893	-0.0813	-0.3359	0.1802	0.0894	0.1802	-0.1528	0.0001	0.316	0.0011	0.0266	0.1963	0.0195	0.2368	52.7147	84.763	208.6578
26	0.004	0.0034	-0.0007	0.0028	0.0001	0.0004	0.0722	-0.2291	0.0134	-0.0453	0.0331	-0.0722	-0.1697	-0.084	0.0002	0.4033	0.1089	-0.0546	0.4056	-0.054	0.2154	10.2892	75.4363	217.7274
27	0.0166	-0.0141	-0.0087	0.0098	0.0062	0.0057	0.0745	-0.0455	0.0952	0.0663	-0.058	0.0291	-0.0634	-0.0124	0	0.1427	0.0206	-0.0122	0.1635	-0.0031	0.1704	52.1495	100.3631	218.2465

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 119 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 120 through 184 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 185 through 215 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 216 through 241 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 242 through 279 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 280 through 325 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 326 through 347 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 97 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 98 through 140 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 141 through 215 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 216 through 241 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 242 through 325 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 326 through 347 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1 through 97 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 98 through 325 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 326 through 347 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 40 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 41 through 140 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 141 through 184 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 185 through 241 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 242 through 279 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 280 through 325 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 326 through 347 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 440 through 447 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 439 through 450 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 440 through 449 )
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 439 through 448 )

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