PDB-4z13: Recombinantly expressed latent aurone synthase (polyphenol oxidas...

ID or keywords:

Entry

Database: PDB / ID: 4z13

Title

Recombinantly expressed latent aurone synthase (polyphenol oxidase) co-crystallized with hexatungstotellurate(VI) and soaked in H2O2

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: 1.78 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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4z13.cif.gz	595 KB	Display	PDBx/mmCIF format
PDB format	pdb4z13.ent.gz	497.7 KB	Display	PDB format
PDBx/mmJSON format	4z13.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4z13_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4z13_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4z13_validation.xml.gz	44.7 KB	Display
Data in CIF	4z13_validation.cif.gz	67.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z1/4z13 ftp://data.pdbj.org/pub/pdb/validation_reports/z1/4z13	HTTPS FTP

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Related structure data

Related structure data	4z0ySC 4z0zC 4z11C 4z12C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4z12-1 4f7b-4 4z14-7 4tw2-1 4tw0-4 6yrx-d 4z11-1 4z11-3 4tw0-3 4z14-8 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) #111 - Mar 2009 Hydrogenase similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 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)	52.880, 109.750, 94.760
Angle α, β, γ (deg.)	90.00, 96.30, 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 , 7 types, 879 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-O / OXYGEN ATOM Mass: 15.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-TEW / 6-tungstotellurate(VI) Mass: 1614.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O₂₄TeW₆
#6: Chemical	ChemComp-W / TUNGSTEN ION Mass: 183.840 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: W
#7: Chemical	ChemComp-TE / TELLURIUM Mass: 127.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Te
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 858 / 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: 2.3 Å³/Da / Density % sol: 46.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 12% PEG 4000, 1 mM hexatungstotellurate(VI), 60 mM sodium citrate, pH 5.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9173 Å / Relative weight: 1
Reflection	Resolution: 1.78→47.41 Å / Num. obs: 101112 / % possible obs: 98.39 % / Redundancy: 3.85 % / R_merge(I) obs: 0.112 / Net I/σ(I): 8.6
Reflection shell	Resolution: 1.78→1.84 Å / Redundancy: 3.89 % / R_merge(I) obs: 1.337 / Mean I/σ(I) obs: 1 / % possible all: 96.15

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4Z0Y

4z0y

Resolution: 1.78→47.415 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1961	5054	5 %
R_work	0.1574	-	-
obs	0.1593	101097	98.38 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.78→47.415 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8004	0	96	858	8958

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	8372
X-RAY DIFFRACTION	f_angle_d	1.038	11508
X-RAY DIFFRACTION	f_dihedral_angle_d	12.522	3025
X-RAY DIFFRACTION	f_chiral_restr	0.039	1181
X-RAY DIFFRACTION	f_plane_restr	0.005	1479

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 (%)
1.78-1.8002	0.336	163	0.3202	3094	X-RAY DIFFRACTION	95
1.8002-1.8214	0.3427	165	0.3112	3138	X-RAY DIFFRACTION	95
1.8214-1.8436	0.3239	165	0.2964	3125	X-RAY DIFFRACTION	98
1.8436-1.867	0.3056	167	0.2844	3190	X-RAY DIFFRACTION	98
1.867-1.8915	0.3281	169	0.2734	3202	X-RAY DIFFRACTION	98
1.8915-1.9174	0.2878	165	0.2617	3158	X-RAY DIFFRACTION	99
1.9174-1.9448	0.2987	170	0.2502	3216	X-RAY DIFFRACTION	99
1.9448-1.9739	0.2772	170	0.2389	3243	X-RAY DIFFRACTION	99
1.9739-2.0047	0.279	169	0.2292	3196	X-RAY DIFFRACTION	99
2.0047-2.0376	0.2825	171	0.2101	3254	X-RAY DIFFRACTION	99
2.0376-2.0727	0.2165	167	0.1983	3185	X-RAY DIFFRACTION	99
2.0727-2.1104	0.2293	166	0.1833	3149	X-RAY DIFFRACTION	96
2.1104-2.151	0.2283	164	0.1866	3103	X-RAY DIFFRACTION	97
2.151-2.1949	0.2185	170	0.1777	3239	X-RAY DIFFRACTION	99
2.1949-2.2426	0.216	168	0.1643	3199	X-RAY DIFFRACTION	100
2.2426-2.2948	0.187	171	0.1517	3251	X-RAY DIFFRACTION	99
2.2948-2.3522	0.1812	168	0.1475	3186	X-RAY DIFFRACTION	99
2.3522-2.4158	0.2044	172	0.1478	3269	X-RAY DIFFRACTION	99
2.4158-2.4869	0.1966	169	0.1436	3197	X-RAY DIFFRACTION	99
2.4869-2.5671	0.1728	168	0.1377	3205	X-RAY DIFFRACTION	99
2.5671-2.6589	0.1716	172	0.1349	3273	X-RAY DIFFRACTION	99
2.6589-2.7653	0.1716	170	0.1368	3222	X-RAY DIFFRACTION	99
2.7653-2.8912	0.1835	169	0.1381	3215	X-RAY DIFFRACTION	99
2.8912-3.0436	0.1914	164	0.1394	3104	X-RAY DIFFRACTION	95
3.0436-3.2342	0.1921	168	0.1422	3199	X-RAY DIFFRACTION	98
3.2342-3.4838	0.1917	171	0.1325	3252	X-RAY DIFFRACTION	100
3.4838-3.8343	0.17	171	0.1319	3255	X-RAY DIFFRACTION	100
3.8343-4.3888	0.1652	172	0.1222	3256	X-RAY DIFFRACTION	99
4.3888-5.5281	0.1529	170	0.1335	3236	X-RAY DIFFRACTION	99
5.5281-47.4316	0.1639	170	0.1538	3232	X-RAY DIFFRACTION	97

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	4.1674	-0.089	0.9617	1.1956	-0.0979	3.071	-0.3596	1.0547	0.1206	-0.2155	0.2224	-0.0777	-0.0378	0.3755	0.0756	0.3816	-0.1073	-0.0107	0.4765	0.0547	0.2315	-14.1987	-11.6265	-64.7021
2	5.8152	-0.4725	-2.2507	2.1374	-0.7712	2.0264	0.3131	0.618	-0.6672	-0.1916	0.0675	0.1323	0.6394	-0.7971	-0.3816	0.3816	-0.1642	-0.082	0.5281	-0.0284	0.4138	-32.2054	-21.2561	-53.7935
3	5.6711	-4.1054	-2.7901	7.1046	2.2812	1.3898	-0.6081	0.0096	-1.3588	0.2466	0.4931	0.5134	0.8504	-1.3279	0.191	0.5395	-0.2598	0.0118	0.5353	0.1289	0.4053	-24.8126	-25.0294	-37.1213
4	2.1818	-0.0576	1.0274	0.7915	0.4316	1.8342	0.0895	0.2537	-0.1775	-0.1164	0.0666	0.0269	0.2979	0.0712	-0.1138	0.2649	-0.0412	0.0209	0.1807	-0.0076	0.1962	-12.9787	-19.7969	-49.1352
5	4.0569	-0.2743	2.06	1.8066	0.0283	3.3465	-0.2465	0.1599	0.3529	0.0118	0.0911	-0.1487	-0.089	0.2032	0.1269	0.2047	-0.0546	0.0251	0.0965	0.0271	0.2149	-4.7218	-4.2654	-38.5922
6	3.5564	2.4827	-0.3262	1.7329	-0.2279	0.0298	0.2299	-1.3766	-0.4364	0.2976	-0.2988	0.4695	0.2221	-0.9465	0.0911	0.5443	-0.3845	-0.0854	1.4383	0.0495	1.3841	-15.7186	4.5487	-59.2699
7	2.8419	-0.3043	-0.7882	1.9408	1.0144	3.3093	-0.1199	0.4459	0.0693	-0.2844	0.1599	-0.0833	0.0921	0.2257	-0.034	0.2163	-0.0449	0.0075	0.2439	0.0041	0.153	-6.1906	-11.9239	-49.0879
8	1.9578	0.3613	1.0435	1.0844	0.3238	1.7962	-0.0766	-0.1695	0.2075	0.008	-0.0048	0.1479	0.0049	-0.2845	0.0715	0.1791	-0.0057	0.0331	0.1874	0.0104	0.2187	-19.722	-7.5738	-38.7395
9	0.355	0.0277	-0.0688	0.1937	0.335	0.5919	-0.2122	0.3711	0.7083	-0.3078	0.1818	-0.042	-0.2595	0.1543	-0.1067	0.5456	-0.1357	-0.2372	0.3131	0.1823	0.967	0.8655	19.9402	-43.8877
10	2.2954	0.0975	0.1404	1.8428	0.4481	1.0376	-0.4123	0.2625	0.8559	-0.2029	0.0717	0.2437	-0.2962	-0.1195	0.1158	0.3267	-0.0553	-0.1023	0.1892	0.0665	0.5363	-5.2878	8.2374	-39.534
11	1.512	0.6943	0.5859	1.2792	0.1466	0.2478	-0.4132	0.2939	0.8837	-0.2487	0.0385	0.1171	-0.4434	0.0574	0.2907	0.4548	-0.0503	-0.1708	0.2953	0.1223	0.7221	-5.6397	13.0489	-42.5027
12	1.1712	0.1997	1.1105	1.3671	0.0949	0.9665	0.1796	-0.4021	-0.2383	0.3083	-0.147	-0.0464	0.2654	-0.1179	0.0837	0.3015	-0.076	-0.0034	0.3398	0.0831	0.2439	26.902	-24.0311	1.9814
13	3.6431	-3.3688	-1.6598	7.5496	2.5573	4.7231	0.6239	1.4233	-0.3595	-1.7385	-0.5853	-0.0865	0.3574	-0.1573	-0.0335	0.4085	0.0184	0.0664	0.4506	-0.0434	0.2344	21.831	-26.8558	-26.3458
14	1.3418	0.2402	0.6334	1.076	0.1265	1.9148	0.1417	-0.2359	-0.2038	0.1444	-0.1181	-0.1256	0.2853	-0.0283	-0.0096	0.1948	-0.0458	0.0148	0.185	0.0493	0.1868	24.6582	-23.9556	-3.6907
15	2.6377	0.4065	-1.1863	5.1241	-1.1737	1.4416	0.1275	-0.1313	-0.4348	-0.1951	-0.0777	0.6007	0.4054	-0.3696	-0.0548	0.2977	-0.1097	-0.0412	0.2457	-0.0241	0.3134	9.266	-29.9864	-14.7981
16	1.3776	0.2049	0.5644	1.1444	-0.1323	1.4541	0.0244	-0.3838	-0.0188	0.1038	-0.1078	0.1821	-0.0049	-0.4055	0.0489	0.1726	-0.0139	0.0449	0.279	-0.0283	0.1994	11.3327	-14.3063	-7.0855
17	1.8848	-0.741	1.0605	1.6063	0.1454	1.882	-0.0132	-0.0695	0.0727	0.0856	-0.1027	-0.2027	-0.1061	0.1498	0.1109	0.1918	-0.0601	0.0188	0.2522	0.0308	0.2183	31.0612	-12.5032	-3.8124
18	6.1947	-5.8	-4.7974	5.5715	4.6005	3.7994	0.4338	1.916	1.186	-1.315	0.3652	0.1778	-1.0733	-1.6713	-0.8343	0.7971	0.1176	0.1612	0.8353	0.206	0.3403	19.7177	-8.7732	-27.8534
19	0.4863	0.1579	-0.7537	0.8627	-0.4723	1.2861	-0.2526	-0.3428	0.199	-0.0023	-0.0275	0.4332	-0.3055	-0.2622	-0.0033	0.2639	0.1474	-0.0381	0.4097	-0.2147	0.4069	1.8084	2.9208	-15.0249
20	0.204	0.0919	-0.3297	0.5363	-0.1405	1.6848	-0.0195	-0.1657	0.1099	0.2671	0.0972	0.0924	-0.2579	-0.1603	-0.3101	0.5196	0.1077	0.3296	1.0115	-0.4233	0.5295	-5.846	-0.4233	8.984
21	1.1809	0.0048	-0.2183	2.7377	-0.1209	0.08	-0.1362	-0.5286	0.293	0.285	-0.1068	0.1204	-0.2635	-0.328	-0.0949	0.465	0.1474	-0.0868	0.5871	-0.306	0.4213	7.7724	7.8469	-0.9574
22	1.3573	0.0449	0.365	1.1026	0.2234	0.4935	-0.115	-0.7844	0.2999	0.3734	-0.1079	0.2068	-0.2146	-0.6739	0.1195	0.3622	0.0836	0.03	0.6504	-0.2327	0.3912	1.9273	-1.7924	-1.6803
23	3.7898	1.1401	-5.0637	4.9522	-3.3815	7.5208	0.0455	-0.6816	-0.4552	0.1703	0.1296	0.171	0.1255	-0.2349	-0.1883	0.3251	-0.0391	-0.0097	0.4173	0.0451	0.3196	-7.905	-19.0674	-24.6591

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)
23	X-RAY DIFFRACTION	23	(chain D and resid 1:1)

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Protein , 1 types, 2 molecules AB

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Protein , 1 types, 2 molecules AB

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Non-polymers , 7 types, 879 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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Yorodumi