PDB-4z12: Recombinantly expressed latent aurone synthase (polyphenol oxidas...

ID or keywords:

Entry

Database: PDB / ID: 4z12

Title

Recombinantly expressed latent aurone synthase (polyphenol oxidase) co-crystallized with hexatungstotellurate(VI)

Components

Aurone synthase

Keywords

OXIDOREDUCTASE / Polyphenol oxidase / Type III copper protein / Latent / Polyoxometalate

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: 1.85 Å

Authors

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

Funding support

Austria, 3items

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	Mar 23, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 30, 2016	Group: Database references
Revision 1.2	Apr 13, 2016	Group: Database references
Revision 1.3	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 1.4	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 / 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_asym_id / _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.ptnr3_auth_asym_id / _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.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
Revision 1.5	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4z12.cif.gz	579.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4z12.ent.gz	486.1 KB	Display	PDB format
PDBx/mmJSON format	4z12.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4z12_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4z12_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4z12_validation.xml.gz	40.9 KB	Display
Data in CIF	4z12_validation.cif.gz	59.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z1/4z12 ftp://data.pdbj.org/pub/pdb/validation_reports/z1/4z12	HTTPS FTP

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Related structure data

Related structure data	4z0ySC 4z0zC 4z11C 4z13C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4z13-1 4z14-7 4z11-2 4z11-1 4z11-3 4z14-5 4z14-2 4z14-8 4z14-3 4udp-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
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (1)

Deposited unit

A: Aurone synthase

B: Aurone synthase

hetero molecules

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

1

A: Aurone synthase

hetero molecules

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

2

B: Aurone synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.990, 110.410, 94.990
Angle α, β, γ (deg.)	90.00, 95.76, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Aurone synthase Mass: 59329.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coreopsis grandiflora (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A075DN54

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Non-polymers , 6 types, 488 molecules

#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-TEW / 6-tungstotellurate(VI) Mass: 1614.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O₂₄TeW₆
#5: Chemical	ChemComp-W / TUNGSTEN ION Mass: 183.840 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: W
#6: Chemical	ChemComp-TE / TELLURIUM Mass: 127.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Te
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 12% PEG 4000, 1 mM hexatungstotellurate(VI), 60 mM sodium citrate, pH 6.4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0247 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 7, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0247 Å / Relative weight: 1
Reflection	Resolution: 1.85→48.14 Å / Num. obs: 90855 / % possible obs: 98.1 % / Redundancy: 4.57 % / R_merge(I) obs: 0.118 / Net I/σ(I): 8.3
Reflection shell	Resolution: 1.85→1.92 Å / Redundancy: 4.76 % / R_merge(I) obs: 2.729 / Mean I/σ(I) obs: 0.6 / % possible all: 96.93

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4Z0Y

4z0y

Resolution: 1.85→48.14 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2049	4542	5 %
R_work	0.1716	-	-
obs	0.1733	90829	98.07 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.85→48.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7954	0	98	470	8522

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	8330
X-RAY DIFFRACTION	f_angle_d	0.986	11422
X-RAY DIFFRACTION	f_dihedral_angle_d	11.91	2982
X-RAY DIFFRACTION	f_chiral_restr	0.038	1184
X-RAY DIFFRACTION	f_plane_restr	0.005	1473

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 (%)
1.85-1.871	0.4368	149	0.4184	2819	X-RAY DIFFRACTION	97
1.871-1.893	0.4218	150	0.3929	2855	X-RAY DIFFRACTION	96
1.893-1.9161	0.338	149	0.364	2834	X-RAY DIFFRACTION	99
1.9161-1.9404	0.3691	150	0.3552	2839	X-RAY DIFFRACTION	97
1.9404-1.9659	0.3637	148	0.3431	2819	X-RAY DIFFRACTION	96
1.9659-1.9928	0.3298	151	0.3268	2863	X-RAY DIFFRACTION	99
1.9928-2.0213	0.3438	150	0.3077	2849	X-RAY DIFFRACTION	97
2.0213-2.0515	0.3154	150	0.288	2848	X-RAY DIFFRACTION	97
2.0515-2.0835	0.2904	152	0.2776	2879	X-RAY DIFFRACTION	99
2.0835-2.1177	0.3056	147	0.2563	2798	X-RAY DIFFRACTION	96
2.1177-2.1542	0.2984	152	0.2469	2877	X-RAY DIFFRACTION	99
2.1542-2.1934	0.2756	151	0.2462	2863	X-RAY DIFFRACTION	97
2.1934-2.2356	0.2522	149	0.2214	2841	X-RAY DIFFRACTION	98
2.2356-2.2812	0.2593	149	0.2076	2856	X-RAY DIFFRACTION	97
2.2812-2.3308	0.2288	151	0.1959	2860	X-RAY DIFFRACTION	98
2.3308-2.385	0.2365	151	0.1912	2885	X-RAY DIFFRACTION	99
2.385-2.4447	0.2659	151	0.1907	2865	X-RAY DIFFRACTION	98
2.4447-2.5108	0.2199	153	0.1808	2903	X-RAY DIFFRACTION	98
2.5108-2.5846	0.2254	150	0.1722	2849	X-RAY DIFFRACTION	99
2.5846-2.6681	0.2252	152	0.1682	2906	X-RAY DIFFRACTION	98
2.6681-2.7634	0.2154	154	0.1734	2919	X-RAY DIFFRACTION	99
2.7634-2.874	0.1864	152	0.1652	2876	X-RAY DIFFRACTION	99
2.874-3.0048	0.2084	152	0.1684	2889	X-RAY DIFFRACTION	99
3.0048-3.1632	0.2238	154	0.1747	2937	X-RAY DIFFRACTION	99
3.1632-3.3614	0.178	153	0.1564	2896	X-RAY DIFFRACTION	99
3.3614-3.6208	0.1571	152	0.141	2900	X-RAY DIFFRACTION	99
3.6208-3.985	0.1812	154	0.1299	2927	X-RAY DIFFRACTION	99
3.985-4.5613	0.1559	154	0.1158	2921	X-RAY DIFFRACTION	99
4.5613-5.7452	0.1584	155	0.1218	2936	X-RAY DIFFRACTION	99
5.7452-48.161	0.1554	157	0.1483	2978	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	4.9216	-1.3745	1.6113	1.982	0.8034	3.9069	-0.11	1.2302	0.21	-0.353	0.1303	-0.2867	-0.0359	0.3941	-0.0109	0.6121	-0.1198	-0.011	0.7935	0.0683	0.4322	-14.8046	-11.4558	-64.5618
2	2.4151	-1.8412	1.8157	2.04	-0.5233	7.9281	0.2162	-0.0573	-0.8536	-0.2951	0.1633	0.3476	0.7462	-1.3794	-0.5469	0.5313	-0.2511	-0.0871	0.8941	0.0813	0.6136	-32.404	-21.0889	-53.3699
3	1.2781	-1.201	1.5901	2.0187	0.9421	8.66	-0.799	0.1764	-1.4404	-0.15	0.3689	1.0933	1.4986	-1.5183	0.4314	0.6486	-0.2587	0.0064	0.7917	0.0171	0.6469	-25.2468	-25.1687	-37.0921
4	2.3928	-0.2884	1.4753	2.0605	0.0217	2.9047	0.1422	0.2309	-0.2143	-0.1225	0.1012	0.0134	0.4372	-0.0991	-0.2275	0.3889	-0.055	0.0168	0.3689	-0.0203	0.2892	-13.4018	-19.6898	-49.0587
5	4.97	-1.6321	2.8518	3.2863	-0.4859	5.2053	-0.2471	0.2065	0.327	0.0614	0.1073	-0.2991	-0.1363	0.2553	0.1189	0.3086	-0.0541	0.0679	0.2131	0.0488	0.302	-5.1767	-4.2714	-38.3383
6	2	2	-2.1283	2	0.2084	1.5936	1.6714	5.3559	0.2934	-20.4017	-8.1964	17.0274	-2.7523	-17.1317	6.5181	1.6099	0.0995	-0.6394	1.385	0.0257	1.2872	-20.9557	4.4797	-60.0062
7	3.0271	-0.3426	0.94	3.1416	1.7347	3.0967	-0.0138	0.3704	0.0282	-0.4534	0.1059	-0.0675	-0.0499	0.2117	-0.099	0.3685	-0.0345	0.021	0.4054	0.0158	0.2656	-6.5387	-11.8958	-48.945
8	1.9169	0.3077	1.518	1.7316	0.5938	2.9862	-0.0846	-0.2199	0.0575	0.0631	0.0569	0.179	0.0824	-0.6304	0.0305	0.3289	-0.0086	0.0614	0.4533	0.0579	0.3408	-20.0049	-7.5518	-38.4394
9	4.1148	-1.0485	-2.1255	4.4547	-1.2718	2.6247	-0.3374	0.5426	1.3925	0.1198	0.0698	-0.406	-0.5251	0.2486	0.17	0.7155	-0.1737	-0.1966	0.5163	0.2576	0.8841	0.3424	20.1683	-43.439
10	3.0871	-0.672	0.5962	3.2354	0.754	2.8935	-0.4478	0.2854	0.4764	-0.2158	0.0956	0.0322	-0.5307	-0.0966	0.2984	0.4791	-0.0498	-0.0757	0.31	0.1069	0.5132	-5.383	8.2501	-39.2797
11	4.3201	0.3674	0.1542	3.9512	0.6932	0.1664	-0.1921	0.7985	1.1446	-0.2814	0.0284	-0.3645	-0.5734	-0.0207	0.1397	0.616	-0.0677	-0.1416	0.4164	0.1833	0.5886	-5.7283	13.3712	-42.4177
12	2.0581	-0.3236	1.8549	2.1906	0.0848	1.6338	0.2883	-0.4649	-0.511	0.3167	-0.1685	0.1121	0.4523	-0.2584	0.0513	0.4427	-0.0967	-0.0159	0.44	0.1178	0.436	26.7575	-24.0638	2.3164
13	9.3451	6.4452	-0.7806	9.6123	-4.7724	3.7501	0.2738	1.581	0.0177	-2.7467	-0.9287	0.0187	1.4498	-1.1736	0.8152	0.8463	0.0962	-0.027	0.6874	-0.1196	0.4678	21.6776	-26.6013	-26.2009
14	3.0669	-0.3493	1.5017	1.6948	-0.3164	1.591	0.3406	-0.1272	-0.5249	0.0981	-0.1304	-0.0729	0.5748	-0.0297	-0.0781	0.3815	-0.0482	-0.0204	0.2036	0.0528	0.3378	24.6232	-23.9591	-3.2666
15	0.5797	-0.2055	-0.7384	4.2446	-0.7843	1.2878	0.5651	-0.1045	-1	-0.2094	0.045	0.8233	0.6024	-0.478	-0.3203	0.5619	-0.1234	-0.2304	0.3891	-0.0096	0.8168	9.3392	-30.1972	-14.139
16	3.2577	-0.4621	1.5041	2.2321	-0.3135	2.9752	0.0245	-0.4332	-0.1788	0.04	-0.0368	0.3242	0.0512	-0.6125	0.0365	0.2476	-0.0218	0.0336	0.3078	-0.0126	0.2901	11.3996	-14.2165	-6.6644
17	3.4495	-0.8825	2.4028	2.0432	-0.9499	4.2562	-0.0307	0.2063	0.1241	0.0354	-0.2347	-0.2346	-0.1494	0.411	0.2481	0.2572	-0.051	0.0306	0.2558	0.0415	0.2898	31.1474	-12.6379	-3.5233
18	8.8799	-6.9928	-4.5264	8.1215	4.4404	2.5997	0.805	1.8089	0.4237	-2.1378	-0.5472	-0.2453	0.3116	0.1361	-0.2808	0.9832	0.2229	-0.0379	0.8095	0.1637	0.3913	19.2708	-8.1299	-27.5279
19	0.8271	-0.5535	-1.3597	1.8181	-0.0248	4.0742	0.0138	-0.0158	0.3881	-0.0448	-0.1886	0.3419	-0.5099	-0.7047	0.0636	0.3799	0.1145	-0.075	0.4076	-0.1773	0.4072	0.4407	3.4764	-13.5723
20	1.6791	1.7143	1.665	2.0847	0.3741	6.7869	0.0048	-0.1392	0.285	0.919	0.093	0.5045	-0.5802	-0.4175	-0.1958	0.7311	0.2516	0.2146	1.1486	-0.2648	0.5492	-5.6518	-0.3244	9.61
21	2.2583	0.3386	0.4486	4.2274	0.0035	0.2432	-0.5187	-0.6027	0.4485	0.375	0.1104	-0.1493	-0.4976	-0.3491	0.21	0.7226	0.226	-0.177	0.5717	-0.2548	0.545	7.3678	8.1561	-0.4875
22	2.5686	0.1562	0.7633	2.2326	-0.0945	1.5199	-0.2184	-0.8243	0.2158	0.3752	0.0819	0.1306	-0.4084	-0.8144	0.1466	0.5034	0.1605	0.0218	0.6943	-0.1482	0.4125	1.9566	-1.6059	-1.3626

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 3:37)
2	X-RAY DIFFRACTION	2	(chain A and resid 38:52)
3	X-RAY DIFFRACTION	3	(chain A and resid 53:56)
4	X-RAY DIFFRACTION	4	(chain A and resid 57:185)
5	X-RAY DIFFRACTION	5	(chain A and resid 186:236)
6	X-RAY DIFFRACTION	6	(chain A and resid 237:244)
7	X-RAY DIFFRACTION	7	(chain A and resid 245:295)
8	X-RAY DIFFRACTION	8	(chain A and resid 296:372)
9	X-RAY DIFFRACTION	9	(chain A and resid 373:399)
10	X-RAY DIFFRACTION	10	(chain A and resid 400:486)
11	X-RAY DIFFRACTION	11	(chain A and resid 487:519)
12	X-RAY DIFFRACTION	12	(chain B and resid 3:61)
13	X-RAY DIFFRACTION	13	(chain B and resid 62:65)
14	X-RAY DIFFRACTION	14	(chain B and resid 66:158)
15	X-RAY DIFFRACTION	15	(chain B and resid 159:188)
16	X-RAY DIFFRACTION	16	(chain B and resid 189:302)
17	X-RAY DIFFRACTION	17	(chain B and resid 303:349)
18	X-RAY DIFFRACTION	18	(chain B and resid 350:354)
19	X-RAY DIFFRACTION	19	(chain B and resid 355:380)
20	X-RAY DIFFRACTION	20	(chain B and resid 381:394)
21	X-RAY DIFFRACTION	21	(chain B and resid 395:424)
22	X-RAY DIFFRACTION	22	(chain B and resid 425:519)

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The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 488 molecules

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-Protein , 1 types, 2 molecules AB

-Non-polymers , 6 types, 488 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 488 molecules

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Details

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Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi