PDB-6i86: Crocagin biosynthetic gene J

ID or keywords:

Entry

Database: PDB / ID: 6i86

Title

Crocagin biosynthetic gene J

Components

Uncharacterized protein

Keywords

BIOSYNTHETIC PROTEIN / CgnJ / domain of unknown function / Crocagin / RiPPs

Function / homology

Uncharacterized protein

Function and homology information

Biological species

Chondromyces crocatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Adam, S. / Koehnke, J.

Funding support

Germany, 1items

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2019
Title: The structure of CgnJ, a domain of unknown function protein from the crocagin gene cluster.
Authors: Adam, S. / Klein, A. / Surup, F. / Koehnke, J.

History

Deposition	Nov 19, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	May 15, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6i86.cif.gz	207 KB	Display	PDBx/mmCIF format
PDB format	pdb6i86.ent.gz	168.2 KB	Display	PDB format
PDBx/mmJSON format	6i86.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6i86_validation.pdf.gz	440.4 KB	Display	wwPDB validaton report
Full document	6i86_full_validation.pdf.gz	441.9 KB	Display
Data in XML	6i86_validation.xml.gz	23.3 KB	Display
Data in CIF	6i86_validation.cif.gz	33.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i8/6i86 ftp://data.pdbj.org/pub/pdb/validation_reports/i8/6i86	HTTPS FTP

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Related structure data

Similar structure data	1bz6-d 3a0z-1 1cfz-2 3a0w-2 3a0z-2 1vxb-d 2gdm-d 1mbn-d 6krc-d 1mbo-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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

hetero molecules

52.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein

hetero molecules

defined by author&software
Evidence: light scattering
17.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Uncharacterized protein

hetero molecules

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

3

C: Uncharacterized protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	132.560, 132.560, 112.980
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Uncharacterized protein Mass: 17497.875 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chondromyces crocatus (bacteria) / Gene: CMC5_025600 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K1EC30
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 444 / 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 grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: ammonium phosphate, tri-sodium citrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 2→57.17 Å / Num. obs: 68297 / % possible obs: 100 % / Redundancy: 7.4 % / R_merge(I) obs: 0.081 / R_pim(I) all: 0.035 / R_rim(I) all: 0.095 / Net I/σ(I): 18.5
Reflection shell	Resolution: 2→2.05 Å / R_merge(I) obs: 0.671 / R_pim(I) all: 0.28 / R_rim(I) all: 0.779

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
xia2		data reduction
xia2		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→57.169 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1985	3484	5.1 %
R_work	0.1748	-	-
obs	0.176	68293	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→57.169 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3707	0	0	444	4151

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3807
X-RAY DIFFRACTION	f_angle_d	0.645	5205
X-RAY DIFFRACTION	f_dihedral_angle_d	7.815	2555
X-RAY DIFFRACTION	f_chiral_restr	0.046	594
X-RAY DIFFRACTION	f_plane_restr	0.004	665

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 (%)
2-2.0274	0.2749	152	0.2378	2539	X-RAY DIFFRACTION	100
2.0274-2.0564	0.2454	134	0.2302	2552	X-RAY DIFFRACTION	100
2.0564-2.0871	0.2201	134	0.2091	2565	X-RAY DIFFRACTION	100
2.0871-2.1197	0.2337	140	0.2125	2536	X-RAY DIFFRACTION	100
2.1197-2.1544	0.2401	125	0.2094	2590	X-RAY DIFFRACTION	100
2.1544-2.1916	0.2836	125	0.2008	2543	X-RAY DIFFRACTION	100
2.1916-2.2314	0.2275	127	0.2046	2604	X-RAY DIFFRACTION	100
2.2314-2.2744	0.2285	134	0.1969	2532	X-RAY DIFFRACTION	100
2.2744-2.3208	0.2206	148	0.194	2576	X-RAY DIFFRACTION	100
2.3208-2.3713	0.2035	151	0.1961	2546	X-RAY DIFFRACTION	100
2.3713-2.4264	0.2092	151	0.1904	2562	X-RAY DIFFRACTION	100
2.4264-2.4871	0.2317	131	0.19	2568	X-RAY DIFFRACTION	100
2.4871-2.5543	0.1977	140	0.1811	2575	X-RAY DIFFRACTION	100
2.5543-2.6295	0.234	138	0.1913	2570	X-RAY DIFFRACTION	100
2.6295-2.7144	0.2117	131	0.186	2590	X-RAY DIFFRACTION	100
2.7144-2.8114	0.2337	131	0.1836	2596	X-RAY DIFFRACTION	100
2.8114-2.9239	0.2009	123	0.1839	2589	X-RAY DIFFRACTION	100
2.9239-3.057	0.2276	142	0.185	2610	X-RAY DIFFRACTION	100
3.057-3.2182	0.2228	141	0.1829	2590	X-RAY DIFFRACTION	100
3.2182-3.4198	0.1901	131	0.1602	2628	X-RAY DIFFRACTION	100
3.4198-3.6838	0.1656	150	0.1542	2593	X-RAY DIFFRACTION	100
3.6838-4.0544	0.1511	146	0.1541	2631	X-RAY DIFFRACTION	100
4.0544-4.6409	0.1641	159	0.1287	2613	X-RAY DIFFRACTION	100
4.6409-5.8461	0.1683	139	0.151	2697	X-RAY DIFFRACTION	100
5.8461-57.1918	0.1934	161	0.1826	2814	X-RAY DIFFRACTION	100

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	8.2007	6.6122	1.6563	5.501	1.0291	1.0325	-0.0858	-0.2208	-0.0684	-0.0776	0.0107	0.0278	0.0965	-0.0799	0.0506	0.1654	0.0204	-0.0141	0.2129	0.0109	0.2196	-21.2836	35.8204	-8.9234
2	7.3283	5.7255	5.8589	8.5377	6.6177	5.704	0.249	-0.1068	-0.1811	-0.1633	-0.2379	0.0071	-0.2364	-0.7949	-0.058	0.2043	0.0203	-0.0057	0.2612	-0.0047	0.2571	-35.2373	39.042	-13.8309
3	3.8149	1.619	3.0285	4.9941	-0.0646	3.9777	0.1466	-0.3551	0.3392	-0.1262	-0.141	0.7445	0.1152	-0.545	0.0133	0.1768	0.0451	0.035	0.3834	0.0095	0.3333	-42.9646	45.8759	-12.2156
4	2.5481	0.3764	0.325	4.1919	1.1922	1.0906	0.0512	-0.1039	-0.1057	-0.0948	-0.0707	0.1692	0.1112	-0.1493	0.0236	0.1716	-0.0071	-0.0051	0.2028	0.0369	0.1314	-28.957	36.8386	-15.3065
5	9.2487	3.2856	4.4295	1.1803	1.0777	7.3082	0.0356	0.5347	-0.6016	-0.1523	0.1608	0.1032	0.3042	0.0855	-0.1766	0.1853	0.0019	-0.0244	0.2206	0.0219	0.2376	-15.0748	38.1245	-20.2544
6	4.7806	1.5743	-0.1312	2.8624	0.1985	3.2226	-0.0031	-0.3188	-0.1304	0.0908	-0.0938	0.2502	0.111	-0.2607	0.0818	0.1977	0.0415	0.0212	0.2601	0.0178	0.2463	-30.7824	41.2556	-8.5906
7	3.1607	3.6485	1.9746	9.3752	5.5108	4.4832	-0.0879	0.1744	-0.0188	-0.3294	0.1217	-0.0248	-0.1249	-0.1004	0.0197	0.1527	0.0187	-0.0188	0.2198	0.036	0.2155	-24.5202	37.7235	-19.2049
8	4.0627	-3.4557	2.7062	4.6732	-3.7972	3.1125	0.0672	-0.3005	-0.8973	0.071	0.1009	0.1863	0.8671	-0.5618	-0.3181	0.393	-0.0981	0.0148	0.3071	0.0462	0.4187	-31.1426	21.0573	-15.3233
9	7.5945	3.9612	0.4165	2.507	1.3481	3.024	-0.1472	-0.0392	-0.1171	-0.1384	0.2229	0.1183	0.1906	0.1476	0.0017	0.1336	0.0358	-0.0259	0.2141	0.0344	0.1381	-21.2721	35.7266	-14.5518
10	1.826	0.3374	1.6794	1.1264	0.8624	2.8477	-0.098	0.1184	0.0566	-0.0557	0.07	0.0045	-0.3429	0.2311	0.0338	0.1687	-0.0238	0.0091	0.1818	-0.0124	0.1325	6.7466	60.4101	-5.395
11	8.9811	6.2402	6.2544	6.7481	4.6153	8.0014	-0.1389	0.944	-0.078	0.0068	0.3819	0.1231	-0.0746	0.5285	-0.2906	0.2424	-0.0292	0.0242	0.4646	0.014	0.1743	10.0337	56.8535	-23.1833
12	5.513	-1.7876	4.0883	7.2988	-3.0918	3.5112	0.4321	0.7724	-0.821	-0.2532	0.0139	-0.1556	0.4311	0.5917	-0.394	0.2	0.0657	-0.0024	0.3835	-0.1045	0.2597	12.5448	47.9142	-17.6398
13	4.9394	1.965	1.9796	1.6317	1.3556	1.7962	0.0082	0.1024	0.08	0.0159	-0.0165	0.0221	-0.1795	-0.0123	0.0322	0.1842	0.0095	-0.0196	0.1526	0.0158	0.133	4.9185	55.5413	-5.757
14	2.2673	3.4672	4.0635	6.7973	6.5708	9.3176	0.2178	-0.6025	0.1947	0.1066	-0.5803	0.5274	0.626	-0.8977	0.3701	0.3029	-0.0096	-0.0738	0.2626	0.0137	0.2444	8.6166	54.0714	8.5
15	5.2355	4.27	-3.5578	7.5447	-4.579	9.2731	-0.0146	0.2618	-0.2865	-0.0436	0.1175	-0.3071	0.0055	0.5462	-0.2279	0.2073	0.0118	-0.0398	0.3064	-0.0544	0.2368	14.8464	52.3756	-3.7993
16	4.0479	5.3059	2.1742	6.9109	2.7541	1.6511	-0.0844	-0.0498	0.1748	-0.1551	0.0523	-0.0715	-0.6428	0.3757	0.0393	0.2848	-0.1171	0.0128	0.3462	0.0362	0.1726	11.8164	63.2078	-12.2887
17	8.0285	7.0246	7.8984	6.4247	6.5556	7.882	-0.5813	0.3769	0.6988	-0.4421	0.1278	0.431	-0.9747	0.3143	0.5198	0.3256	-0.0618	-0.0369	0.2687	0.0488	0.2508	7.0668	63.5953	-12.6337
18	3.2371	4.4616	0.7636	6.5993	0.2016	2.2094	0.2576	-0.3813	-0.2197	0.3188	-0.209	0.1059	0.0966	-0.1155	-0.0505	0.2383	0.0145	-0.0142	0.1866	-0.0131	0.0756	3.174	53.2547	-0.9251
19	5.2724	-4.4877	4.4987	3.8949	-3.9359	4.1029	-0.3024	-0.7332	0.1011	0.4328	0.2948	0.6825	-0.8085	-0.8488	0.0591	0.3574	0.077	0.0017	0.3827	-0.0834	0.3966	-7.8477	61.7394	-1.3568
20	3.7902	2.4231	4.9788	2.3793	2.0022	7.9641	0.1126	0.4562	-0.2281	-0.0082	0.0257	-0.1113	0.1225	0.2569	-0.1534	0.2277	-0.0154	-0.0087	0.1358	-0.0209	0.1501	17.0143	57.7714	1.17
21	2.6852	0.0841	-0.4371	1.0219	-0.3567	2.5753	0.0328	-0.2209	-0.3955	0.1505	0.0098	-0.0315	0.2057	0.0191	-0.0637	0.19	0.0137	-0.0445	0.1823	0.0293	0.2247	-5.7308	30.5768	-5.6192
22	7.9195	-2.4611	3.9093	4.7671	-5.0919	6.2657	-0.2124	-0.5776	0.2306	0.8496	0.1337	-0.6322	-0.5477	0.1881	0.1119	0.2567	0.0003	-0.049	0.242	-0.0347	0.2146	-4.7105	39.6018	2.3117
23	1.1305	0.4881	-1.5156	7.6836	-7.5129	8.4064	-0.1202	-0.0707	0.0021	0.0588	0.0399	-0.1386	0.1289	-0.0299	0.0965	0.1292	0.0079	-0.053	0.1973	0.008	0.2286	0.4263	36.923	-6.2376
24	3.5089	-0.9904	1.9498	2.1936	-1.2105	2.8386	0.1055	0.1102	-0.1344	-0.0848	-0.1297	-0.417	0.0996	0.4418	0.0319	0.2012	0.0355	-0.0318	0.2374	-0.0291	0.3299	9.6669	28.7318	-8.0876
25	5.1706	-5.6734	4.4271	9.818	-6.5637	4.5953	0.1228	-0.3966	-0.8453	0.076	0.1038	0.3714	0.282	-0.1985	-0.3407	0.237	-0.0209	-0.0435	0.2248	0.0724	0.3093	-4.8887	24.4715	-3.4957
26	4.8284	-1.3572	0.413	5.0703	-1.9541	1.8998	0.0085	-0.1126	-0.4999	0.2279	0.0332	-0.036	0.1523	0.1158	-0.0455	0.2027	0.0267	-0.0284	0.1914	-0.0284	0.1804	0.0013	26.8299	-5.3523
27	3.8732	2.0793	1.5116	8.7702	1.8604	2.4378	-0.0402	0.7071	-0.187	-0.7683	-0.042	-0.3447	0.0492	0.3093	0.047	0.2706	0.0542	0.0661	0.3636	-0.0242	0.2857	4.4691	33.8916	-22.9354
28	5.7062	-1.0828	2.7193	6.9057	-2.6604	2.5729	-0.0206	-0.6172	-0.4576	0.6926	-0.1104	-0.7451	0.0058	0.4271	0.0813	0.2793	0.0793	-0.0981	0.3441	0.0405	0.3786	9.419	23.9008	-0.8931

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 12 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 20 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 21 through 45 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 46 through 67 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 68 through 79 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 80 through 112 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 113 through 128 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 129 through 138 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 139 through 153 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid -1 through 20 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 21 through 35 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 36 through 45 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 46 through 67 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 68 through 79 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 80 through 88 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 89 through 97 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 98 through 112 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 113 through 131 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 132 through 145 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 146 through 154 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 2 through 35 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 36 through 45 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 46 through 57 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 58 through 88 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 89 through 97 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 98 through 121 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 122 through 145 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 146 through 154 )

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-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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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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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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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