PDB-3hhs: Crystal Structure of Manduca sexta prophenoloxidase

ID or keywords:

Entry

Database: PDB / ID: 3hhs

Title

Crystal Structure of Manduca sexta prophenoloxidase

Components

Phenoloxidase subunit 1
Phenoloxidase subunit 2

Keywords

OXIDOREDUCTASE / alpha helix / beta strand / Melanin biosynthesis / Metal-binding / Monooxygenase / Secreted

Function / homology

Function and homology information

positive regulation of melanization defense response / melanin biosynthetic process from tyrosine / tyrosinase / tyrosinase activity / chloride ion binding / defense response / copper ion binding / extracellular region
Similarity search - Function

Biological species

Manduca sexta (tobacco hornworm)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.97 Å

Authors

Li, Y. / Wang, Y. / Jiang, H. / Deng, J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structure of Manduca sexta prophenoloxidase provides insights into the mechanism of type 3 copper enzymes.
Authors: Li, Y. / Wang, Y. / Jiang, H. / Deng, J.

History

Deposition	May 17, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 29, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3hhs.cif.gz	305.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3hhs.ent.gz	252.5 KB	Display	PDB format
PDBx/mmJSON format	3hhs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3hhs_validation.pdf.gz	442.2 KB	Display	wwPDB validaton report
Full document	3hhs_full_validation.pdf.gz	457.8 KB	Display
Data in XML	3hhs_validation.xml.gz	58.7 KB	Display
Data in CIF	3hhs_validation.cif.gz	88.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hh/3hhs ftp://data.pdbj.org/pub/pdb/validation_reports/hh/3hhs	HTTPS FTP

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Related structure data

Similar structure data	4yzw-d 4l7i-1 5uj7-2 3hws-3 2d73-d 4n0f-3 20285 4k0b-1 6s3u-2 3edj-d 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: Phenoloxidase subunit 2

B: Phenoloxidase subunit 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	148.832, 153.664, 75.763
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-826- HOH

#1: Protein	Phenoloxidase subunit 2 / proPO-p2 Mass: 80026.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: tissue / Source: (natural) Manduca sexta (tobacco hornworm) / References: UniProt: Q25519, tyrosinase
#2: Protein	Phenoloxidase subunit 1 / proPO-P1 Mass: 78933.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: tissue / Source: (natural) Manduca sexta (tobacco hornworm) / References: UniProt: O44249, tyrosinase
#3: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1195 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.73 Å³/Da / Density % sol: 54.86 %
Crystal grow	Temperature: 298 K / Method: sitting drop / pH: 7.5 / Details: PEG10000, pH 7.5, sitting drop, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2008

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Relative weight: 1

Reflection

Resolution: 1.97→50 Å / Num. obs: 121340 / % possible obs: 100 % / Redundancy: 8.3 % / R_merge(I) obs: 0.105 / Net I/σ(I): 28.646

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.97-2.03	7.6	0.928	1	100
2.03-2.07	8.2	0.81	1	100
2.07-2.11	8.4	0.716	1	100
2.11-2.15	8.4	0.601	1	100
2.15-2.2	8.5	0.522	1	100
2.2-2.25	8.5	0.462	1	100
2.25-2.31	8.5	0.382	1	100
2.31-2.37	8.5	0.34	1	100
2.37-2.44	8.5	0.299	1	100
2.44-2.52	8.5	0.251	1	100
2.52-2.61	8.5	0.213	1	100
2.61-2.71	8.5	0.186	1	100
2.71-2.84	8.5	0.148	1	100
2.84-2.99	8.5	0.124	1	100
2.99-3.17	8.4	0.099	1	100
3.17-3.42	8.4	0.082	1	100
3.42-3.76	8.2	0.075	1	100
3.76-4.31	8.1	0.067	1	100
4.31-5.43	7.9	0.05	1	100
5.43-50	7.9	0.038	1	99.2

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	42.43 Å
Translation	2.5 Å	42.43 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	1.3.3	phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.005	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.97→42.45 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.953 / Occupancy max: 1 / Occupancy min: 0 / SU B: 5.868 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.194	6106	5 %	RANDOM
R_work	0.154	-	-	-
obs	0.156	121340	98.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 17.22 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	0 Å²	0 Å²
2-	-	0.03 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.97→42.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10786	0	4	1195	11985

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	11011
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.516	1.947	14907
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.082	5	1326
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.833	23.55	555
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.886	15	1825
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.177	15	88
X-RAY DIFFRACTION	r_chiral_restr	0.116	0.2	1582
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	8551
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	5042
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.307	0.2	7500
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	1187
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.192	0.2	34
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.166	0.2	29
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.869	1.5	6879
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.31	2	10809
X-RAY DIFFRACTION	r_scbond_it	2.472	3	4738
X-RAY DIFFRACTION	r_scangle_it	3.577	4.5	4095
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.97→2.02 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	433	-
R_work	0.225	8108	-
obs	-	-	95.61 %

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	3.3646	0.2656	-0.7362	2.5327	-0.4589	1.3163	0.0189	0.101	-0.0643	-0.1296	-0.0042	0.2281	0.0773	-0.0893	-0.0148	0.0488	-0.0242	-0.0377	0.0211	-0.0138	0.1718	-38.4774	41.0103	-0.3223
2	9.2253	-0.8008	-3.1807	4.6913	3.2741	14.6722	0.0391	0.685	0.5326	-0.4724	0.1772	0.3556	-0.2424	-0.688	-0.2163	0.1077	-0.04	-0.0636	0.107	0.024	0.3015	-47.4021	43.4223	-7.5401
3	1.7972	0.5227	0.4942	1.9329	0.3324	1.2525	0.0481	-0.1264	-0.1668	0.0254	-0.0733	0.0209	0.1385	-0.0109	0.0252	0.0961	-0.0028	0.0068	0.0685	0.0106	0.2013	-25.1079	37.3443	6.0561
4	1.673	0.7353	-0.2043	15.2199	1.2938	2.1555	-0.0721	0.1299	-0.1034	-0.4532	0.0885	-0.3982	0.1376	0.0233	-0.0164	0.0902	0.0064	0.0115	0.1211	-0.0162	0.1745	-22.2425	46.4564	-5.9817
5	7.3273	1.4688	2.2953	2.4205	1.016	1.2398	-0.0315	0.3976	-0.1446	-0.1067	0.0753	0.0397	-0.0294	0.012	-0.0438	0.1274	0.0173	-0.0024	0.1118	-0.0146	0.1595	-31.2204	64.3428	-9.8605
6	2.0277	-0.9257	0.1067	3.8912	-0.5849	1.0276	0.0538	0.0259	-0.0953	0.062	-0.0434	-0.0249	0.0326	0.0156	-0.0105	0.0341	0.0029	-0.01	0.0806	-0.0297	0.0867	-9.6453	55.6827	-2.0593
7	0.9596	0.0463	-0.0476	0.7492	0.0575	0.3839	0.0142	-0.0806	0.0013	0.0743	-0.0313	0.016	-0.0052	0.0311	0.017	0.0576	0.0041	-0.0106	0.0719	-0.0021	0.1202	-5.5919	58.2348	7.0634
8	3.1237	0.0825	0.8688	2.0317	0.712	2.5261	0.0069	-0.2125	-0.3566	0.2413	-0.0021	-0.1037	0.2037	0.1462	-0.0048	0.1255	0.0176	-0.0306	0.0882	0.0509	0.2315	7.4324	42.896	13.582
9	11.4816	-2.668	3.3636	18.0129	3.0207	8.4221	0.0064	-0.392	-0.2522	0.465	0.1098	0.713	0.3422	-0.2825	-0.1162	0.1671	-0.0016	-0.0033	0.1324	0.0882	0.2349	2.5471	40.9163	16.9973
10	1.3081	-0.3038	-0.2263	0.5414	0.1271	0.6866	0.0068	0.0474	-0.0594	0.0021	-0.0075	-0.0708	0.0528	0.042	0.0007	0.0666	-0.0001	-0.0125	0.0544	0.0001	0.1605	0.953	53.9412	0.8478
11	1.2191	-0.0447	0.0027	0.6883	-0.083	0.482	0.039	0.2825	-0.1353	-0.1115	-0.0254	-0.068	0.0739	0.0603	-0.0137	0.078	0.0298	-0.0026	0.0904	-0.0325	0.0843	-1.6228	54.2635	-17.8173
12	14.5062	-6.6855	-1.4784	5.9151	3.8585	13.7124	-0.0488	0.5422	-0.5763	-0.1098	0.0529	0.7198	0.387	-1.0492	-0.0041	-0.0154	-0.0136	-0.0447	0.062	-0.0262	0.1048	-17.542	50.7279	-15.9481
13	2.7531	-0.8753	-0.2729	2.2429	-0.4582	1.1387	-0.0019	0.2217	-0.4623	-0.0782	-0.0411	0.1819	0.2266	-0.0174	0.0429	0.0929	0.0182	-0.015	0.0985	-0.0762	0.0969	0.8272	49.0497	-15.7718
14	1.0147	-0.2778	0.019	1.0583	-0.4365	1.2705	-0.0081	0.2089	-0.1916	-0.0552	-0.0346	-0.1771	0.0611	0.0844	0.0427	0.1057	0.0429	0.0211	0.1327	-0.0474	0.2203	10.9126	46.9534	-11.6036
15	11.3889	0.4454	-1.045	2.3028	-0.0481	2.1737	-0.0281	0.575	0.3336	-0.1721	0.0053	0.1997	0.0074	-0.2463	0.0229	0.1935	0.0178	0.0057	0.1845	0.0233	0.0818	-9.5562	64.8579	-22.0573
16	1.5369	-0.2041	-0.0604	2.9346	1.4677	3.6283	0.056	0.0778	-0.0702	-0.0551	-0.038	0.2452	-0.1732	-0.0898	-0.018	0.0686	-0.0023	-0.0246	0.0876	0.0343	0.1349	-48.6976	72.5039	-8.5972
17	1.918	0.4816	0.6704	1.8803	0.4785	1.7243	-0.0348	0.1354	0.0742	-0.1596	0.067	0.1627	-0.1781	-0.0687	-0.0322	0.152	0.0101	0.0199	0.0667	0.0379	0.1275	-43.488	84.4132	-2.3548
18	1.113	-0.0287	-0.0019	1.6827	0.5697	1.674	-0.0067	-0.1258	-0.1455	0.2122	0.0304	0.1117	0.056	-0.0591	-0.0236	0.1043	0.0071	0.039	0.0974	0.0384	0.2127	-41.7073	62.6352	11.3808
19	0.8251	-0.0306	-0.088	3.3174	-0.2754	1.8563	-0.062	-0.0695	0.0389	0.0291	0.1063	-0.0068	-0.0738	-0.0155	-0.0444	0.0805	0.0139	0.0433	0.1371	-0.0021	0.0689	-36.5304	82.9751	20.7295
20	0.7365	-0.3408	-0.1807	0.9837	0.1149	1.3505	-0.0361	-0.1355	0.008	0.0989	0.0825	-0.0936	-0.063	0.1109	-0.0464	0.0955	0.0175	0.0091	0.1085	-0.0002	0.0959	-23.6306	79.0299	19.6882
21	3.427	-2.2353	-2.0314	6.0527	3.2022	1.9711	-0.0609	-0.2367	0.1984	0.2836	0.0366	-0.2527	-0.3264	0.0484	0.0243	0.2543	-0.0138	0.0219	0.1126	-0.0472	0.161	-21.298	101.8942	23.3268
22	3.3299	-0.1578	-1.0086	2.688	-0.4342	3.5786	0.1462	-0.1968	0.5687	0.3645	0.0193	0.0752	-0.7956	-0.0489	-0.1655	0.3067	0.0483	0.0497	0.0743	-0.039	0.1937	-32.231	103.4159	21.9087
23	0.6409	0.0865	-0.149	0.6597	-0.2798	0.9171	-0.0225	-0.1674	0.0875	0.2147	0.1138	0.0281	-0.1921	-0.0591	-0.0913	0.1235	0.0454	0.0263	0.0991	-0.0114	0.0753	-29.5376	88.6864	24.354
24	0.1446	-0.1909	0.3259	0.8809	1.4174	6.1616	-0.0115	-0.1508	-0.1331	0.1395	0.0276	0.0822	0.146	-0.2153	-0.016	0.1238	0.0082	0.0552	0.169	0.0552	0.1691	-46.2988	65.7238	23.1628
25	1.0051	0.1402	-0.2428	1.8634	0.0291	1.9984	-0.0575	-0.1938	0.0135	0.3523	0.1888	0.2836	-0.2123	-0.3121	-0.1313	0.2828	0.1729	0.1282	0.2734	0.0633	0.0937	-48.3184	85.9649	41.2396
26	8.7186	0.9822	-2.6984	0.1495	-0.8988	9.9325	0.2337	0.6171	-0.2929	0.2116	0.0765	0.5616	-0.009	-1.3048	-0.3102	0.1435	0.0566	0.0554	0.3079	0.0479	0.2005	-51.4439	78.7164	18.8216
27	0.6251	0.2878	-0.3808	1.3307	-0.1431	2.3567	-0.0819	-0.1559	0.0781	0.3813	0.1425	0.1796	-0.1698	-0.2193	-0.0606	0.2085	0.1159	0.0952	0.2565	0.04	0.0911	-45.3295	83.2076	37.6574
28	8.0417	-10.5258	7.5267	13.7983	-9.9497	7.4996	1.6863	0.2977	-1.9535	-2.3782	-1.1794	3.0045	1.028	-1.0702	-0.5069	0.4664	0.3231	-0.0694	0.4456	-0.0258	0.596	-55.9912	92.2084	22.2142
29	0.8114	-0.2213	-0.6557	1.8827	-0.6129	2.457	-0.026	-0.2163	0.0951	0.3939	0.1925	0.086	-0.4141	-0.2099	-0.1665	0.274	0.1404	0.0953	0.2466	0.0038	0.1065	-42.3449	90.8264	38.8184
30	9.5267	3.3617	9.0399	14.5827	3.4653	32.5247	0.1648	-0.6476	-0.4374	-0.1187	-0.2979	1.0023	1.1346	-2.2387	0.1332	0.2728	0.0219	0.0054	0.2605	0.0261	0.2535	-45.7705	60.6809	31.8258

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 50
2	X-RAY DIFFRACTION	2	A	51 - 60
3	X-RAY DIFFRACTION	3	A	61 - 141
4	X-RAY DIFFRACTION	4	A	142 - 162
5	X-RAY DIFFRACTION	5	A	165 - 191
6	X-RAY DIFFRACTION	6	A	192 - 230
7	X-RAY DIFFRACTION	7	A	231 - 317
8	X-RAY DIFFRACTION	8	A	318 - 357
9	X-RAY DIFFRACTION	9	A	358 - 364
10	X-RAY DIFFRACTION	10	A	365 - 449
11	X-RAY DIFFRACTION	11	A	453 - 560
12	X-RAY DIFFRACTION	12	A	561 - 566
13	X-RAY DIFFRACTION	13	A	567 - 633
14	X-RAY DIFFRACTION	14	A	634 - 676
15	X-RAY DIFFRACTION	15	A	677 - 693
16	X-RAY DIFFRACTION	16	B	3 - 53
17	X-RAY DIFFRACTION	17	B	54 - 141
18	X-RAY DIFFRACTION	18	B	142 - 185
19	X-RAY DIFFRACTION	19	B	186 - 237
20	X-RAY DIFFRACTION	20	B	238 - 310
21	X-RAY DIFFRACTION	21	B	311 - 330
22	X-RAY DIFFRACTION	22	B	332 - 356
23	X-RAY DIFFRACTION	23	B	357 - 439
24	X-RAY DIFFRACTION	24	B	440 - 480
25	X-RAY DIFFRACTION	25	B	481 - 554
26	X-RAY DIFFRACTION	26	B	555 - 583
27	X-RAY DIFFRACTION	27	B	584 - 613
28	X-RAY DIFFRACTION	28	B	617 - 625
29	X-RAY DIFFRACTION	29	B	626 - 674
30	X-RAY DIFFRACTION	30	B	675 - 680

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