PDB-3l2k: Structure of phenazine antibiotic biosynthesis protein with substrate

ID or keywords:

Entry

Database: PDB / ID: 3l2k

Title

Structure of phenazine antibiotic biosynthesis protein with substrate

Components

EhpF

Keywords

BIOSYNTHETIC PROTEIN / PHENAZINE / ANTIBIOTIC / PDC

Function / homology

ANL, N-terminal domain / phenazine-1,6-dicarboxylic acid / EhpF

Function and homology information

Biological species

Pantoea agglomerans (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Bera, A.K. / Atanasova, V. / Parsons, J.F.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure of the D-alanylgriseoluteic acid biosynthetic protein EhpF, an atypical member of the ANL superfamily of adenylating enzymes.
Authors: Bera, A.K. / Atanasova, V. / Gamage, S. / Robinson, H. / Parsons, J.F.

History

Deposition	Dec 15, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 26, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Mar 21, 2012	Group: Database references
Revision 1.3	Sep 6, 2023	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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3l2k.cif.gz	151.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3l2k.ent.gz	123.6 KB	Display	PDB format
PDBx/mmJSON format	3l2k.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/l2/3l2k ftp://data.pdbj.org/pub/pdb/validation_reports/l2/3l2k	HTTPS FTP

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Related structure data

Related structure data	3hguSC 3hgvC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ez5-2 6boo-1 2r2l-d 2zir-d 3hgu-d 3mfi-d 3oha-d 3hgv-d 1n95-d 2hvh-1 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: EhpF

B: EhpF

hetero molecules

82.3 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)	193.129, 193.129, 193.129
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	197
Space group name H-M	I23

#1: Protein	EhpF Mass: 40903.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pantoea agglomerans (bacteria) / Gene: ehpF / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GPH0
#2: Chemical	ChemComp-PXC / phenazine-1,6-dicarboxylic acid Mass: 268.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₈N₂O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.67 Å³/Da / Density % sol: 66.48 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Na/K Phosphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 105 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 13, 2008
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.8→48.28 Å / Num. obs: 29538 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / R_merge(I) obs: 0.1 / Net I/σ(I): 12
Reflection shell	Resolution: 2.8→2.9 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2930 / R_sym value: 0.5

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Processing

Software

Name	Version	Classification
CrystalClear		data collection
PHASER		phasing
REFMAC	5.2.0019	refinement
d*TREK		data reduction
d*TREK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3HGU

3hgu

Resolution: 2.8→26.78 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.898 / SU B: 30.471 / SU ML: 0.273 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.583 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2881	1495	5.1 %	RANDOM
R_work	0.21207	-	-	-
obs	0.21635	27888	99.89 %	-

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: 36.45 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→26.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5538	0	40	16	5594

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.03	0.022	5721
X-RAY DIFFRACTION	r_angle_refined_deg	2.713	1.963	7792
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.767	5	704
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.864	23.755	261
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.246	15	935
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.68	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.176	0.2	867
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	4392
X-RAY DIFFRACTION	r_nbd_refined	0.294	0.2	2818
X-RAY DIFFRACTION	r_nbtor_refined	0.349	0.2	3940
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.196	0.2	223
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.235	0.2	33
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.191	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.015	1.5	3612
X-RAY DIFFRACTION	r_mcangle_it	1.787	2	5714
X-RAY DIFFRACTION	r_scbond_it	2.697	3	2507
X-RAY DIFFRACTION	r_scangle_it	4.32	4.5	2077

LS refinement shell

Resolution: 2.8→2.877 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.318	119
R_work	0.25	2013

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	34.3861	-21.7153	-8.0995	23.1187	-11.3541	30.7459	0.949	0.0888	4.4171	0.8635	-0.8247	-1.4479	0.2759	-1.4783	-0.1243	0.1622	-0.1286	-0.0592	0.2746	-0.1038	0.3653	51.192	36.559	55.837
2	20.3288	-14.612	-7.0804	18.9142	-4.1658	12.6497	0.04	-0.4379	-1.2138	0.433	0.8184	-1.2886	-2.2518	1.7879	-0.8583	0.3559	-0.1174	0.0905	0.1853	0.0934	-0.0117	51.825	32.52	64.134
3	6.5767	-0.8015	-5.6155	6.7798	15.4086	37.2397	-2.1383	-0.8853	0.0607	0.1341	2.0441	-0.7389	-0.503	-0.2954	0.0942	0.657	0.1041	-0.0232	-0.0428	0.2469	0.3921	47.283	32.002	72.982
4	2.6948	-0.977	0.1315	4.4145	-2.1897	2.7194	-0.0031	0.4103	0.7706	-0.0729	0.2037	-0.0468	-1.1279	-0.3103	-0.2006	0.1867	0.1928	-0.0026	0.2117	0.116	0.269	39.856	31.89	58.79
5	11.8997	-3.2712	-3.5906	3.436	0.415	1.2124	0.0806	0.2126	0.4773	-0.2678	-0.3606	0.4116	-0.0961	-1.0257	0.28	0.2506	0.2446	-0.045	0.1689	0.0817	0.1725	31.057	30.855	62.497
6	4.8539	-5.1059	-2.0218	5.9463	3.7556	8.3303	-0.0803	0.3043	-0.3012	-0.1293	-0.8384	0.8602	-0.3496	-1.1738	0.9187	0.0151	0.1385	-0.0136	0.3865	0.067	0.1856	32.496	19.24	58.518
7	1.8835	0.513	0.5646	16.9709	2.5217	9.9954	-0.1458	0.1953	-0.3104	-0.384	0.2116	-0.2027	-0.7504	0.232	-0.0658	-0.0095	0.1718	0.0705	0.27	0.0797	0.0403	46.041	19.07	51.797
8	4.914	-1.0065	2.7805	0.2703	-1.0159	4.6811	0.0144	-0.0298	0.1055	-0.0757	-0.123	-0.1678	-0.1994	-0.2931	0.1087	0.306	0.1025	0.0904	0.1383	0.037	0.1532	49.143	15.275	60.879
9	15.6695	-9.5507	1.7569	20.9989	17.7447	23.5224	-1.2138	-0.0232	-0.4668	0.5988	1.6305	-0.6684	-0.5924	0.3104	-0.4167	0.1103	0.1433	0.0525	0.208	0.1112	0.1588	66.405	13.71	74.435
10	0.0098	-0.052	-0.0925	1.3072	-0.1213	1.2272	0.0036	0.0403	0.0821	-0.0568	-0.0859	0.1182	-0.0876	-0.1098	0.0823	0.1638	0.0293	0.0515	0.2662	-0.0144	0.1982	55.711	4.118	59.887
11	35.4035	-21.4442	-9.8511	45.6088	-11.9656	12.5994	-0.8623	1.9744	-0.5987	0.7853	2.1187	0.9364	-0.1146	-0.543	-1.2564	0.1436	-0.3494	-0.0929	0.2772	0.1873	0.3175	38.424	-10.719	59.752
12	6.5654	2.964	12.638	21.5213	10.9384	25.6839	1.119	-0.1726	-0.1104	2.2505	-1.1294	1.2517	1.1083	0.199	0.0104	0.2294	-0.137	0.1339	0.2405	0.0123	0.2413	49.3	-13.35	59.536
13	3.3342	2.7266	-1.4312	2.3232	-0.7775	2.2643	-0.0953	-0.0322	0.0153	0.0962	0.0782	-0.1041	0.3275	-0.0742	0.0171	0.1846	-0.0051	0.0347	0.2396	0.0014	0.2055	59.358	-5.731	64.686
14	0.6086	1.2683	-2.6748	2.6434	-5.5746	11.7563	-0.0997	-0.1101	-0.8052	-0.8534	0.1544	0.2002	0.3398	0.3458	-0.0546	0.2347	-0.023	0.0687	0.1397	-0.0252	0.2742	58.253	-13.349	70.656
15	3.2983	-0.5677	-1.5892	2.155	0.4863	3.2535	0.0529	-0.122	0.015	0.0481	-0.0781	-0.0572	-0.0365	-0.0359	0.0253	0.1256	-0.0151	0.0378	0.2216	-0.0058	0.1998	56.634	-2.922	76.752
16	2.0299	-1.0763	3.5458	1.3183	-2.8518	7.4568	0.151	0.2595	-0.1496	0.1169	-0.0902	0.0056	-0.2425	-0.1242	-0.0608	0.1793	0.1104	0.0318	0.2749	-0.0386	0.2079	48.522	8.371	76.061
17	0.9106	-0.6293	1.6893	1.9409	-1.9195	3.5095	0.6864	-0.5852	0.3631	0.1062	-0.6217	0.4658	-0.3563	0.5485	-0.0647	0.2704	0.1623	0.0088	0.275	-0.0514	0.2318	43.002	18.645	72.258
18	7.2657	0.3009	-1.3781	1.2885	-0.3127	0.3126	0.0135	0.1844	-0.0178	0.2523	-0.3753	0.3946	-0.3552	-0.8951	0.3618	0.2169	0.1827	0.0286	0.4495	0.0171	0.1489	30.85	13.414	79.712
19	4.3151	3.9512	-1.3042	13.2518	-7.7013	4.7894	-0.1641	0.6529	-0.0838	-0.2131	0.1501	-0.1577	-0.0682	-0.5328	0.014	0.139	0.1524	0.0193	0.3371	-0.0333	0.1775	39.479	20.133	64.094
20	3.3185	-0.927	2.2018	13.2798	3.0482	7.9311	-0.1093	0.0623	-0.0804	0.0913	0.177	-0.2369	-0.0216	-0.6611	-0.0677	0.043	0.0268	0.0508	0.2487	0.008	0.111	39.238	10.41	77.429
21	2.6661	2.2115	2.5751	2.8328	3.2723	4.6973	-0.3285	0.0823	0.2959	-0.29	0.0322	0.3043	-0.9701	-0.1937	0.2963	0.2744	0.0104	0.0072	0.1436	0.0532	0.2336	79.085	16.066	39.333
22	1.5038	-0.512	-0.1853	0.899	-1.0948	1.873	-0.0809	-0.0461	0.0726	-0.0443	0.0447	0.0745	0.0135	0.1636	0.0362	0.2385	0.0024	0.0093	0.2395	0.0078	0.1566	82.931	4.397	42.914
23	2.0648	-0.9369	-0.6252	0.4552	0.0329	2.2775	0.0732	-0.1004	-0.1934	-0.1982	-0.0856	0.1936	0.1397	0.0043	0.0125	0.248	-0.0246	0.0248	0.1535	0.0117	0.1779	80.233	-2.87	44.431
24	15.1412	3.0876	5.0253	8.8129	1.1524	1.6698	0.5077	-1.0144	0.7624	-0.0704	-0.7797	0.7452	-0.4552	-0.3239	0.272	0.2416	0.0607	0.1629	0.2945	0.0293	0.0775	66.16	7.877	52.583
25	23.1871	-36.6768	-27.14	58.0146	42.9295	31.7668	-3.897	1.4642	-4.1005	-2.6355	-0.7987	-1.312	2.7309	-3.6498	4.6956	0.6057	-0.3698	0.0783	0.5262	-0.0945	0.5497	61.038	-11.167	50.477
26	1.8143	-0.8405	0.6708	2.1236	-2.0285	1.9494	-0.0368	-0.0105	0.1317	0.0178	-0.1604	0.0431	-0.1276	-0.4197	0.1972	0.2218	-0.0068	0.0132	0.2552	-0.0096	0.1389	64.327	7.826	41.797
27	4.0215	-0.2254	4.6247	0.0126	-0.2592	5.3184	-1.1065	0.6767	-0.7178	0.2092	0.3248	2.0494	-2.2059	0.4111	0.7817	0.5364	0.1276	-0.27	0.664	0.2463	0.1342	54.105	18.282	29.275
28	1.287	-0.5391	-0.5405	1.6864	-1.3831	2.0006	-0.0109	0.0563	-0.0423	0.0715	-0.0563	-0.0971	-0.1759	-0.3919	0.0672	0.1398	0.0458	-0.0564	0.3082	-0.0128	0.1548	51.125	5.365	44.72
29	10.967	2.3113	2.7007	42.6947	7.31	4.5107	-0.7917	-0.1757	-1.86	0.2325	-0.0136	0.2704	0.7308	0.9389	0.8053	0.2215	0.038	0.0568	0.2878	-0.2307	0.2539	49.842	-17.443	48.201
30	2.7124	-1.2347	2.1655	0.5726	-0.8931	2.5477	-0.002	0.5876	-0.7543	-0.1002	0.271	1.1507	-0.1184	-0.0356	-0.269	0.0531	-0.092	-0.1582	0.4244	-0.0406	0.3435	39.028	-5.576	45.687
31	4.0704	-1.4568	-0.0159	7.1418	2.9957	1.3505	-0.3777	0.1603	0.2764	-0.1687	0.5827	0.2502	0.1109	-0.4527	-0.205	0.1339	0.0064	-0.1086	0.4279	0.0777	0.1836	42.224	5.034	38.366
32	57.1766	16.3786	-5.751	4.9456	-3.2297	10.4395	0.5328	0.59	-0.0788	0.2094	-0.4993	2.4609	1.2226	0.4195	-0.0335	0.0256	0.0636	-0.1592	0.4227	-0.1801	0.3589	36.512	-4.735	35.984
33	7.6126	-2.1884	6.3178	6.4196	-3.8214	7.3375	-0.0505	-0.0828	-0.0986	-0.3016	0.3836	0.558	-0.1393	-0.5269	-0.3331	0.0511	0.0797	-0.1379	0.3725	-0.0561	0.1634	39.777	4.345	33.481
34	11.1178	17.561	2.7845	39.4138	5.4079	0.7847	1.2402	-0.4695	-2.2622	2.1275	-1.4115	0.3833	0.9216	-0.7265	0.1713	0.1503	-0.0627	-0.1133	0.4085	-0.1637	0.2465	47.418	-6.626	26.488
35	2.5924	1.2486	-1.6968	2.0797	0.3813	2.0825	-0.1245	0.1442	-0.1833	-0.201	0.3862	0.2857	-0.3857	-0.2556	-0.2617	0.1542	0.0401	-0.1152	0.4037	-0.0595	0.1173	45.821	1.449	27.718
36	2.4335	0.1858	4.7395	1.2726	0.1299	10.4348	-0.1547	0.3092	0.218	-0.1935	-0.0519	0.3135	-0.2292	0.1904	0.2066	0.206	0.0359	-0.0245	0.3341	-0.0462	0.1199	57.653	0.537	27.597
37	0.8077	-0.3086	-0.7323	4.2906	0.1175	0.9511	0.2432	0.2082	-0.1981	-0.2298	-0.0873	-0.0651	0.0067	-0.0597	-0.1559	0.2098	0.0272	-0.0406	0.3211	-0.023	0.1327	71.552	-6.369	28.869
38	2.0727	-0.7825	-0.2191	0.4761	-0.125	0.262	0.2703	0.0785	-0.4973	-0.2714	-0.1509	-0.3527	-0.0234	0.286	-0.1195	0.2591	-0.0273	-0.0517	0.301	-0.0406	0.1984	68.374	-8.402	30.874
39	3.1142	1.1483	3.0912	3.7173	2.0948	3.3452	0.0598	0.2222	-0.0493	-0.1057	0.0259	0.0787	-0.1204	0.2411	-0.0857	0.1368	0.0084	0.0252	0.2511	0.0079	0.1105	70.012	-1.881	32.769
40	12.4633	0.1832	-1.8196	10.2974	-4.0326	9.9151	0.2388	0.2929	-0.8372	-1.3732	0.6267	1.8587	1.4956	-0.0402	-0.8655	0.2907	0.0015	-0.1038	0.0978	-0.1463	0.1885	59.624	-12.085	30.424

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 7
2	X-RAY DIFFRACTION	2	A	8 - 13
3	X-RAY DIFFRACTION	3	A	14 - 22
4	X-RAY DIFFRACTION	4	A	23 - 40
5	X-RAY DIFFRACTION	5	A	41 - 60
6	X-RAY DIFFRACTION	6	A	61 - 78
7	X-RAY DIFFRACTION	7	A	79 - 99
8	X-RAY DIFFRACTION	8	A	100 - 123
9	X-RAY DIFFRACTION	9	A	124 - 130
10	X-RAY DIFFRACTION	10	A	131 - 170
11	X-RAY DIFFRACTION	11	A	171 - 184
12	X-RAY DIFFRACTION	12	A	185 - 189
13	X-RAY DIFFRACTION	13	A	190 - 213
14	X-RAY DIFFRACTION	14	A	214 - 224
15	X-RAY DIFFRACTION	15	A	225 - 261
16	X-RAY DIFFRACTION	16	A	262 - 285
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28	X-RAY DIFFRACTION	28	B	131 - 171
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31	X-RAY DIFFRACTION	31	B	199 - 213
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38	X-RAY DIFFRACTION	38	B	308 - 317
39	X-RAY DIFFRACTION	39	B	318 - 346
40	X-RAY DIFFRACTION	40	B	347 - 354

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