PDB-4kvv: Crystal structure of an alkylated Cys mutant of CC-Hex

ID or keywords:

Entry

Database: PDB / ID: 4kvv

Title

Crystal structure of an alkylated Cys mutant of CC-Hex

Components

6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

Keywords

DE NOVO PROTEIN / De novo coiled-coil assembly

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Burton, A.J. / Agnew, C. / Brady, R.L. / Woolfson, D.N.

Citation

Journal: J.Am.Chem.Soc. / Year: 2013
Title: Accessibility, Reactivity, and Selectivity of Side Chains within a Channel of de Novo Peptide Assembly.
Authors: Burton, A.J. / Thomas, F. / Agnew, C. / Hudson, K.L. / Halford, S.E. / Brady, R.L. / Woolfson, D.N.

History

Deposition	May 23, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 11, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4kvv.cif.gz	196.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4kvv.ent.gz	176.1 KB	Display	PDB format
PDBx/mmJSON format	4kvv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kv/4kvv ftp://data.pdbj.org/pub/pdb/validation_reports/kv/4kvv	HTTPS FTP

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Related structure data

Related structure data	4kvtC 4kvuC 3r3k C: citing same article (ref.)
Similar structure data	4kvu-1 4h8o-d 3r48-d 3r47-1 6zt1-1 3r46-d 4pn8-1 3r3k-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details)

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

B: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

C: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

D: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

E: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

F: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

G: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

H: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

I: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

J: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

K: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

L: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

41.4 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

B: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

C: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

D: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

E: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

F: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

defined by author&software
20.7 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

H: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

I: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

J: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

K: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

L: 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation

defined by author&software
20.7 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	56.020, 56.020, 286.500
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein/peptide	6-HELIX COILED COIL CC-HEX-L24C PEPTIDE with an alkylated Cys mutation Mass: 3451.889 Da / Num. of mol.: 12 / Source method: obtained synthetically
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.71 Å³/Da / Density % sol: 54.67 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris, 1.5 M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

Diffraction	Mean temperature: 68 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013
Radiation	Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 1.9→36.34 Å / Num. obs: 37509 / % possible obs: 100 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5

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Processing

Software

Name	Version	Classification
DNA		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→36.34 Å / SU ML: 0.22 / σ(F): 1.27 / Phase error: 22.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2317	3444	5.02 %
R_work	0.2033	-	-
obs	0.2048	37373	99.9 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→36.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2646	0	0	128	2774

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	2646
X-RAY DIFFRACTION	f_angle_d	1.313	3471
X-RAY DIFFRACTION	f_dihedral_angle_d	12.301	977
X-RAY DIFFRACTION	f_chiral_restr	0.055	414
X-RAY DIFFRACTION	f_plane_restr	0.006	423

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 (%)
1.9-1.926	0.3464	150	0.3053	2655	X-RAY DIFFRACTION	100
1.926-1.9536	0.3018	125	0.2829	2575	X-RAY DIFFRACTION	100
1.9536-1.9827	0.3115	156	0.2601	2619	X-RAY DIFFRACTION	100
1.9827-2.0137	0.2505	130	0.2271	2613	X-RAY DIFFRACTION	100
2.0137-2.0467	0.2561	123	0.218	2583	X-RAY DIFFRACTION	100
2.0467-2.082	0.2482	140	0.2166	2685	X-RAY DIFFRACTION	100
2.082-2.1199	0.2517	127	0.2037	2547	X-RAY DIFFRACTION	100
2.1199-2.1606	0.243	121	0.2025	2663	X-RAY DIFFRACTION	100
2.1606-2.2047	0.1992	169	0.1798	2547	X-RAY DIFFRACTION	100
2.2047-2.2526	0.2057	156	0.1771	2605	X-RAY DIFFRACTION	100
2.2526-2.305	0.1783	134	0.1608	2596	X-RAY DIFFRACTION	100
2.305-2.3627	0.2207	129	0.1688	2605	X-RAY DIFFRACTION	100
2.3627-2.4265	0.2415	149	0.1808	2625	X-RAY DIFFRACTION	100
2.4265-2.4979	0.1953	130	0.1827	2596	X-RAY DIFFRACTION	100
2.4979-2.5785	0.2254	138	0.1768	2584	X-RAY DIFFRACTION	100
2.5785-2.6707	0.1968	161	0.177	2627	X-RAY DIFFRACTION	100
2.6707-2.7776	0.2556	106	0.1843	2615	X-RAY DIFFRACTION	100
2.7776-2.9039	0.2958	160	0.2138	2592	X-RAY DIFFRACTION	100
2.9039-3.0569	0.2027	156	0.1971	2596	X-RAY DIFFRACTION	100
3.0569-3.2484	0.2102	160	0.2077	2557	X-RAY DIFFRACTION	100
3.2484-3.499	0.2733	140	0.2271	2638	X-RAY DIFFRACTION	100
3.499-3.8508	0.2153	119	0.1827	2588	X-RAY DIFFRACTION	100
3.8508-4.4071	0.1943	133	0.1735	2632	X-RAY DIFFRACTION	100
4.4071-5.5493	0.2688	109	0.2299	2605	X-RAY DIFFRACTION	99
5.5493-36.3466	0.2199	123	0.2502	2603	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	1.7554	1.3592	0.802	1.4134	-0.4339	2.4348	-0.1101	0.136	0.177	-0.0401	-0.0041	-0.1047	-0.414	0.7797	0.14	0.1972	-0.0211	0.015	0.2559	-0.0005	0.2289	27.0377	43.6956	15.1126
2	3.6484	-3.8626	3.2356	9.1308	-7.9009	6.9191	0.1142	-0.38	0.5197	1.0897	-0.3414	-0.7509	-1.4941	2.1998	0.4587	0.3201	-0.0974	-0.0875	0.5909	-0.0371	0.3139	29.7047	38.1048	36.1746
3	1.9012	0.7958	1.528	2.278	2.2072	2.537	-0.1259	0.0527	0.1866	-0.3066	0.1276	-0.0634	-1.2508	0.2383	0.0422	0.2995	-0.0586	0.043	0.1885	-0.014	0.2382	20.6916	50.3616	15.0374
4	2.6456	2.1003	-2.4078	2.3901	-0.6278	8.6675	-0.1048	-0.786	-0.2895	0.9667	-0.4051	-1.0376	-0.6691	0.0034	0.4312	0.4288	-0.0383	-0.0535	0.3192	0.0225	0.4154	27.2153	49.857	34.9495
5	2.3671	-0.4969	0.7724	1.8629	-0.5257	2.2045	0.1213	0.1085	-0.0406	-0.2446	0.0022	-0.1962	0.7705	0.9376	-0.0468	0.2238	0.0514	0.0059	0.2393	-0.0116	0.2098	24.3125	34.932	16.2711
6	5.2592	-0.7043	-4.5948	8.3593	4.5512	6.0737	-0.8338	-1.1302	-0.9724	1.5621	0.6942	-0.571	1.4712	1.3127	0.2862	0.4514	0.0541	-0.0606	0.4315	0.0543	0.3312	21.7035	32.9011	36.1948
7	1.6047	0.9211	0.1809	3.5004	2.926	2.8429	0.0194	0.1742	-0.0988	-0.0093	0.071	-0.0029	0.157	-0.5194	-0.0788	0.1868	0.017	0.0168	0.2178	0.0069	0.2139	9.1667	39.4135	16.8616
8	3.2816	2.6131	2.5715	4.7382	4.3319	4.1511	-0.2548	-0.6773	-0.4188	1.7931	-0.4581	0.707	0.478	-0.5031	0.5975	0.5287	-0.0244	0.0755	0.2669	-0.0413	0.3044	9.8458	48.4007	36.5554
9	1.2442	-0.5126	-0.5816	2.4961	0.1819	2.5312	0.0608	0.0649	-0.1196	-0.0559	0.0001	0.073	0.6694	-0.038	0.1026	0.2322	-0.0244	0.0235	0.1435	0.0031	0.2085	15.489	32.8604	17.2476
10	3.6547	-3.7441	1.4268	7.9913	4.351	8.778	0.4893	-1.4368	-0.8552	1.7375	-0.3956	-0.0095	0.3521	0.237	-0.0343	0.5723	-0.102	0.0636	0.4621	0.0128	0.2868	12.1588	37.1908	37.0555
11	2.2488	0.1048	0.7689	2.4428	2.9205	8.7457	-0.0299	0.096	0.0862	-0.2283	-0.214	0.2643	-0.7042	-0.4329	0.3426	0.2426	0.0439	0.0159	0.1481	-0.0077	0.2406	11.6802	48.2506	15.6069
12	2.3929	-2.7424	1.9047	7.0744	-0.5254	2.4546	-0.4361	-0.3865	0.1512	1.5344	0.1079	-0.0897	0.0736	-0.3396	0.5349	0.4306	-0.0289	0.0065	0.2068	-0.0814	0.3067	18.6401	55.1153	34.7377
13	0.9819	-1.1718	-0.7886	2.3905	-0.8892	9.4481	0.0853	0.0221	0.0738	-0.0156	0.0375	0.0053	-0.8023	0.4707	-0.0003	0.2344	-0.0681	-0.0076	0.2397	0.0115	0.2322	43.437	23.5967	16.2277
14	5.0717	4.9907	-5.8666	4.9891	-5.7115	6.7787	0.1877	-0.7253	-0.1326	0.9154	-0.1692	-0.2488	0.0055	-0.1374	0.0623	0.3507	0.0252	-0.0222	0.3275	0.0013	0.3089	45.515	18.3193	36.1194
15	2.2191	-0.8875	-1.7477	1.6723	0.4181	2.2719	0.1257	0.1539	0.1257	0.0112	-0.1573	0.2182	-0.8245	-0.4963	0.0681	0.2524	0.0218	0.0236	0.2016	0.002	0.2646	34.5137	24.5078	15.2474
16	3.6549	-4.7548	3.5083	6.1269	-4.6988	4.4152	-0.0158	-0.4373	0.5871	1.2255	-0.0297	-0.6472	-0.3339	-0.0464	0.3042	0.459	-0.084	0.0327	0.3526	-0.0939	0.3784	38.514	25.2874	36.9069
17	2.149	0.3188	-0.2115	1.482	-0.8442	2.554	0.048	0.055	-0.0056	0.091	-0.1224	-0.0507	-0.3428	1.1925	0.0622	0.1901	0.0057	0.0005	0.3215	0.0283	0.2307	47.2439	15.1916	16.1678
18	9.4815	4.7026	-7.0529	2.7499	-2.4641	9.509	-0.2448	-1.2676	-0.0755	0.8273	-0.1139	-0.3336	-0.6582	0.9842	0.2968	0.3708	0.121	-0.0045	0.3752	0.0793	0.2971	43.0804	8.05	36.067
19	2.0041	0.4187	-2.9539	2.9127	-0.7334	9.4454	-0.093	0.2224	-0.1831	-0.1479	-0.0678	-0.0156	0.6684	-0.3893	0.2707	0.221	-0.0583	0.0294	0.2079	-0.0002	0.2676	32.8279	8.6196	14.2842
20	4.9821	1.1584	3.3815	5.1723	5.1887	6.3947	0.9005	-1.181	0.0552	0.8218	-0.354	-0.086	0.3842	-0.6274	-0.6816	0.3286	-0.1238	0.0811	0.5436	0.0656	0.4578	26.3391	11.7684	33.9833
21	2.6317	-0.7897	-1.8003	1.0925	-1.4441	8.0397	-0.1818	0.0291	-0.2746	-0.1479	-0.144	0.0186	0.877	0.3984	0.4665	0.2621	0.034	0.0315	0.1839	0.0041	0.2589	42.02	7.677	15.099
22	9.7757	-2.6745	-1.9916	7.3125	2.5347	2.1451	0.2251	-1.2845	-0.5865	0.4577	-0.1591	-0.5225	0.4321	-0.2193	-0.0937	0.3934	-0.0287	-0.0301	0.331	0.0835	0.354	32.768	4.3046	34.5451
23	2.9789	1.4735	-0.5378	1.0619	-0.5886	8.9126	0.0128	0.4423	-0.0844	0.0201	0.048	0.1218	0.3002	-1.1738	-0.1052	0.168	0.0171	0.0197	0.2919	-0.0191	0.2422	29.0559	17.0284	14.2583
24	3.9107	-2.7664	-2.5379	2.7384	3.6277	9.5526	0.3106	-0.8092	0.0755	0.5435	-0.1001	0.2477	0.1287	0.2375	-0.159	0.275	-0.0134	0.1028	0.3042	-0.0257	0.2674	28.5614	22.7089	35.445

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1 : 20 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 21 : 29 )
3	X-RAY DIFFRACTION	3	CHAIN B AND (RESID 1 : 20 )
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESID 21 : 28 )
5	X-RAY DIFFRACTION	5	CHAIN C AND (RESID 1 : 20 )
6	X-RAY DIFFRACTION	6	CHAIN C AND (RESID 21 : 27 )
7	X-RAY DIFFRACTION	7	CHAIN D AND (RESID 1 : 20 )
8	X-RAY DIFFRACTION	8	CHAIN D AND (RESID 21 : 29 )
9	X-RAY DIFFRACTION	9	CHAIN E AND (RESID 1 : 20 )
10	X-RAY DIFFRACTION	10	CHAIN E AND (RESID 21 : 28 )
11	X-RAY DIFFRACTION	11	CHAIN F AND (RESID 1 : 20 )
12	X-RAY DIFFRACTION	12	CHAIN F AND (RESID 21 : 29 )
13	X-RAY DIFFRACTION	13	CHAIN G AND (RESID 1 : 20 )
14	X-RAY DIFFRACTION	14	CHAIN G AND (RESID 21 : 28 )
15	X-RAY DIFFRACTION	15	CHAIN H AND (RESID 1 : 20 )
16	X-RAY DIFFRACTION	16	CHAIN H AND (RESID 21 : 30 )
17	X-RAY DIFFRACTION	17	CHAIN I AND (RESID 1 : 20 )
18	X-RAY DIFFRACTION	18	CHAIN I AND (RESID 21 : 29 )
19	X-RAY DIFFRACTION	19	CHAIN J AND (RESID 1 : 20 )
20	X-RAY DIFFRACTION	20	CHAIN J AND (RESID 21 : 28 )
21	X-RAY DIFFRACTION	21	CHAIN K AND (RESID 1 : 20 )
22	X-RAY DIFFRACTION	22	CHAIN K AND (RESID 21 : 29 )
23	X-RAY DIFFRACTION	23	CHAIN L AND (RESID 1 : 20 )
24	X-RAY DIFFRACTION	24	CHAIN L AND (RESID 21 : 30 )

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