PDB-9f8o: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c...

ID or keywords:

Entry

Database: PDB / ID: 9f8o

Title

Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl]{2-[(2-morpholinoethyl)amino]phenyl}methanone

Components

Phenazine biosynthesis protein A/B

Keywords

BIOSYNTHETIC PROTEIN / pyocyanin / phenazine biosynthesis / virulence / inhibitor / ketosteroid-isomerase / cocrystal / PhzA/B / Burkholderia cepacia

Function / homology

Phenazine biosynthesis protein A/B / Phenazine biosynthesis protein A/B / antibiotic biosynthetic process / NTF2-like domain superfamily / : / ACETATE ION / Phenazine biosynthesis protein A/B

Function and homology information

Biological species

Burkholderia lata (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.57 Å

Authors

Thiemann, M. / Zimmermann, M. / Kunick, C. / Blankenfeldt, W.

Funding support

1items

Citation

Journal: J.Med.Chem. / Year: 2025
Title: From Bones to Bugs: Structure-Based Development of Raloxifene-Derived Pathoblockers That Inhibit Pyocyanin Production in Pseudomonas aeruginosa.
Authors: Thiemann, M. / Zimmermann, M. / Diederich, C. / Zhan, H. / Lebedev, M. / Pletz, J. / Baumgarten, J. / Handke, M. / Musken, M. / Breinbauer, R. / Krasteva-Christ, G. / Zanin, E. / Empting, M. ...

History

Deposition	May 6, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9f8o.cif.gz	398.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9f8o.ent.gz		Display	PDB format
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Validation report

Summary document	9f8o_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	9f8o_full_validation.pdf.gz	1.8 MB	Display
Data in XML	9f8o_validation.xml.gz	37.3 KB	Display
Data in CIF	9f8o_validation.cif.gz	48.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f8/9f8o ftp://data.pdbj.org/pub/pdb/validation_reports/f8/9f8o	HTTPS FTP

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Related structure data

Related structure data	9f8hC 9f8iC 9f8jC 9f8kC 9f8lC 9f8mC 9f8nC 9f8pC 9f8qC 9f8rC 9f8sC C: citing same article (ref.)
Similar structure data	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	#44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: Phenazine biosynthesis protein A/B

B: Phenazine biosynthesis protein A/B

C: Phenazine biosynthesis protein A/B

D: Phenazine biosynthesis protein A/B

hetero molecules

88.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phenazine biosynthesis protein A/B

B: Phenazine biosynthesis protein A/B

hetero molecules

defined by author&software
Evidence: gel filtration
44.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Phenazine biosynthesis protein A/B

D: Phenazine biosynthesis protein A/B

hetero molecules

defined by author&software
Evidence: gel filtration
44.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.830, 69.629, 83.141
Angle α, β, γ (deg.)	90.00, 90.12, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Phenazine biosynthesis protein A/B Mass: 21531.025 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia lata (bacteria) / Gene: Bcep18194_B1568 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q396C9
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-A1IAF / [2-(4-hydroxyphenyl)-6-oxidanyl-1-benzothiophen-3-yl]-[2-(2-morpholin-4-ylethylamino)phenyl]methanone / [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl]{2-[(2-morpholinoethyl)amino]phenyl}methanone Mass: 474.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₂₆N₂O₄S / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 18.3% (w/v) PEG 3350, 0.1 M Bis-TRIS pH 6.56, 0.133 M lithium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 22, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.57→68.83 Å / Num. obs: 109154 / % possible obs: 99 % / Redundancy: 7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.059 / R_pim(I) all: 0.024 / R_rim(I) all: 0.063 / Net I/σ(I): 14
Reflection shell	Resolution: 1.57→1.59 Å / Redundancy: 7 % / R_merge(I) obs: 0.634 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5405 / CC_1/2: 0.938 / R_pim(I) all: 0.254 / R_rim(I) all: 0.684 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
XDS	Jan 10, 2022	data reduction
Aimless	v0.7.7	data scaling
PHASER	v2.8.3	phasing
PHENIX	v1.20.1-4487	refinement
autoPROC	v1.0.5 (20211020)	data processing
PDB_EXTRACT	v4.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.57→53.07 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1827	5505	5.06 %
R_work	0.1637	-	-
obs	0.1647	108813	98.69 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 27.86 Å²

Refinement step

Cycle: LAST / Resolution: 1.57→53.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5057	0	188	526	5771

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5590
X-RAY DIFFRACTION	f_angle_d	0.791	7590
X-RAY DIFFRACTION	f_dihedral_angle_d	17.737	2050
X-RAY DIFFRACTION	f_chiral_restr	0.061	710
X-RAY DIFFRACTION	f_plane_restr	0.008	1018

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 (%)
1.57-1.58	0.3106	191	0.2819	3390	X-RAY DIFFRACTION	98
1.58-1.6	0.2586	190	0.2441	3451	X-RAY DIFFRACTION	99
1.6-1.62	0.2658	178	0.2329	3425	X-RAY DIFFRACTION	99
1.62-1.64	0.2134	152	0.2135	3451	X-RAY DIFFRACTION	99
1.64-1.67	0.2392	221	0.2041	3427	X-RAY DIFFRACTION	99
1.67-1.69	0.2056	168	0.1936	3465	X-RAY DIFFRACTION	99
1.69-1.71	0.2296	190	0.1848	3418	X-RAY DIFFRACTION	99
1.71-1.74	0.2074	180	0.1758	3437	X-RAY DIFFRACTION	99
1.74-1.76	0.2315	169	0.1771	3495	X-RAY DIFFRACTION	99
1.76-1.79	0.1887	168	0.1745	3410	X-RAY DIFFRACTION	99
1.79-1.82	0.1911	190	0.1798	3443	X-RAY DIFFRACTION	99
1.82-1.86	0.2027	189	0.1785	3467	X-RAY DIFFRACTION	99
1.86-1.89	0.2093	174	0.1798	3465	X-RAY DIFFRACTION	99
1.89-1.93	0.2136	190	0.1758	3419	X-RAY DIFFRACTION	99
1.93-1.97	0.2116	207	0.162	3412	X-RAY DIFFRACTION	99
1.97-2.02	0.1899	208	0.1606	3397	X-RAY DIFFRACTION	99
2.02-2.07	0.1773	161	0.1545	3437	X-RAY DIFFRACTION	97
2.07-2.13	0.1895	213	0.1576	3266	X-RAY DIFFRACTION	95
2.13-2.19	0.1798	178	0.1538	3421	X-RAY DIFFRACTION	98
2.19-2.26	0.1706	177	0.1534	3474	X-RAY DIFFRACTION	99
2.26-2.34	0.1858	195	0.1561	3441	X-RAY DIFFRACTION	99
2.34-2.43	0.1666	186	0.1512	3442	X-RAY DIFFRACTION	99
2.43-2.55	0.178	181	0.1521	3468	X-RAY DIFFRACTION	99
2.55-2.68	0.1868	136	0.1582	3566	X-RAY DIFFRACTION	99
2.68-2.85	0.1621	228	0.1521	3425	X-RAY DIFFRACTION	99
2.85-3.07	0.1522	154	0.1566	3504	X-RAY DIFFRACTION	99
3.07-3.38	0.1919	193	0.1608	3504	X-RAY DIFFRACTION	99
3.38-3.86	0.1779	194	0.1443	3415	X-RAY DIFFRACTION	97
3.86-4.87	0.1288	197	0.1317	3415	X-RAY DIFFRACTION	97
4.87-53.07	0.2045	147	0.2035	3558	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	6.837	-3.4798	1.4311	5.2694	-1	3.08	-0.0746	-0.1782	0.1033	0.1852	0.0239	-0.4169	-0.1273	1.1273	0.1199	0.2251	-0.0428	0.0179	0.5569	-0.0106	0.174	-17.9804	19.5246	-12.6707
2	4.7062	-3.8085	-3.3015	3.5961	3.4232	3.4655	0.2505	0.264	0.0998	-0.2865	-0.2088	0.0835	-0.5841	-0.0563	-0.0322	0.3008	-0.0039	0.011	0.321	0.0176	0.1882	-31.5808	23.6245	-22.9871
3	3.1215	-0.0064	-5.2957	1.2507	-0.1085	9.2222	-0.3315	0.2568	-0.5373	-0.0709	0.0329	-0.0457	0.5988	-0.1062	0.3337	0.1973	-0.0139	0.0079	0.2315	-0.0457	0.1709	-37.0543	10.0324	-13.8224
4	3.6432	-4.8763	-2.5759	8.0126	1.1713	5.4479	0.0991	0.3761	-0.0521	-0.5649	-0.0848	0.1076	-0.0604	-0.2561	0.0584	0.2228	-0.0268	-0.0135	0.3286	-0.0343	0.1612	-38.6132	17.4922	-23.3333
5	4.2063	-1.5981	0.9734	1.7871	-0.8199	3.0453	0.033	0.1161	0.1725	-0.083	-0.027	-0.0698	-0.2262	0.2339	0.0052	0.1662	-0.0279	0.0107	0.1593	-0.0046	0.1011	-30.1805	22.8524	-8.0332
6	4.9811	-0.6438	-1.0807	1.0422	-1.0579	5.1912	-0.0023	0.7029	0.4101	-0.3018	0.0939	0.1634	0.0319	-1.0824	-0.0639	0.2467	0.0595	-0.0398	0.447	0.0357	0.2057	-51.9965	23.7266	-16.1108
7	1.5996	0.0324	-0.6005	0.6384	-0.1529	2.784	0.0182	0.067	0.0397	0.0475	0.0198	0.0409	-0.0928	-0.2546	-0.07	0.1562	-0.0017	-0.003	0.1752	-0.0058	0.1132	-41.3381	19.034	-3.9716
8	9.0522	4.4567	0.1171	5.9011	-1.1559	3.1875	-0.0848	-0.0702	-0.5019	-0.1474	-0.0248	-0.4984	0.0972	0.8551	0.1088	0.1918	0.0505	-0.0158	0.4614	-0.0022	0.1731	-17.7088	13.5119	10.6165
9	4.6185	2.5198	2.2575	6.749	3.8001	4.3271	0.0486	-0.8391	-0.6024	0.3114	-0.1057	-0.01	0.3547	0.0273	-0.0164	0.214	0.0318	0.0056	0.4626	0.1401	0.2138	-31.0556	9.7283	20.7869
10	3.9488	1.2878	5.1703	1.6906	1.4745	7.152	-0.2398	-0.3768	0.5261	0.0295	-0.0249	0.0301	-0.4913	-0.0425	0.3225	0.1941	0.0146	-0.0084	0.2665	-0.0538	0.1615	-36.3908	23.1011	12.7267
11	4.5779	5.0654	4.5969	5.9406	4.6427	5.1917	-0.1206	-0.3172	0.1559	0.293	-0.0316	0.2968	-0.1447	0.0555	0.1287	0.2418	0.0269	-0.0015	0.387	0.001	0.1834	-38.3079	15.5855	21.4291
12	3.5794	1.3025	-1.4026	1.6528	-0.8368	2.1822	-0.0967	-0.1448	-0.1933	0.0307	0.0061	-0.0885	0.137	0.2396	0.1045	0.1579	0.031	-0.01	0.1726	0.0145	0.1126	-30.2099	9.9958	5.922
13	4.5897	1.0957	-0.2558	1.0346	0.1443	1.7625	-0.0316	-0.2243	-0.1491	0.0432	-0.0129	-0.0086	0.02	0.0491	0.0359	0.155	0.0236	0.006	0.1505	0.0084	0.0974	-38.9475	13.2606	8.2248
14	0.671	-0.7618	2.2573	1.5538	-3.3179	8.3888	-0.0105	0.5181	0.0307	-0.1977	0.1648	0.101	0.3412	-0.8306	-0.0155	0.2149	-0.0472	-0.0227	0.4831	-0.0162	0.2193	-52.6997	12.6844	-11.113
15	6.7036	-4.5457	-0.4109	6.1054	-0.8318	3.8932	-0.1043	-0.4042	0.3207	0.0891	0.0625	-0.4424	-0.0702	0.7292	0.0901	0.1899	-0.0572	0.01	0.3719	-0.0125	0.1612	-51.8086	19.2833	-53.9932
16	5.9853	-4.4758	-3.3992	4.2182	3.7854	3.7234	0.1331	0.4556	0.1369	-0.2041	-0.2038	0.1765	-0.2741	-0.1065	0.1012	0.2392	-0.0241	-0.0006	0.3284	0.0242	0.1731	-65.3497	23.6204	-64.1552
17	4.665	-1.4231	-4.699	2.095	1.3267	4.7793	-0.3039	0.4167	-0.5747	-0.0681	-0.0171	0.0658	0.3762	-0.182	0.3462	0.1831	-0.0291	0.0061	0.264	-0.0535	0.1621	-71.3385	10.203	-55.841
18	4.2779	-4.8038	-2.4765	5.633	1.9088	5.0702	0.029	0.5825	-0.2752	-0.4452	-0.1557	0.3945	0.2057	-0.2761	0.1099	0.2537	-0.0181	-0.0231	0.3635	-0.023	0.1963	-72.9218	17.9108	-65.036
19	3.8729	-1.3829	1.0566	1.8652	-0.9812	2.6525	-0.0534	0.1089	0.2122	-0.0196	0.0198	-0.0533	-0.1666	0.1767	0.0437	0.1609	-0.0302	0.0101	0.1725	0.0145	0.1165	-64.106	22.5668	-49.4168
20	4.4759	-1.2161	-0.7908	1.0479	0.2127	2.1045	-0.0409	0.1958	0.0718	0.0064	0.015	0.0264	-0.0272	-0.1384	0.0234	0.1775	-0.0205	-0.0077	0.1865	0.0021	0.1175	-72.9846	19.6917	-51.5717
21	0.5127	0.7303	-1.6132	2.8889	-4.8933	8.7094	0.0069	-0.2202	0.024	0.2585	0.1644	0.1264	-0.3203	-1.1343	-0.1582	0.1872	0.0522	0.0333	0.3388	-0.0043	0.1821	-86.899	19.843	-32.1246
22	3.4191	3.0353	-1.5794	3.541	-1.0773	2.5147	-0.2267	-0.1203	-0.3306	-0.1265	0.0161	-0.382	0.1712	1.1792	0.1137	0.2161	0.0566	-0.0183	0.5922	0.0086	0.1953	-52.7637	12.665	-30.855
23	3.6006	3.3349	-0.4421	3.1978	-0.3395	0.1462	0.0692	-0.6904	-0.3152	0.0735	-0.1874	-0.1547	0.0934	0.284	0.0734	0.2392	0.0305	0	0.4171	0.0725	0.1834	-65.9026	8.8009	-20.7863
24	3.6078	0.2815	4.6871	2.2967	-0.2805	6.7402	-0.3206	-0.3138	0.5655	0.1129	0.0316	0.0227	-0.5632	-0.0297	0.3476	0.212	0.0158	0.0003	0.2538	-0.0489	0.1809	-71.0972	22.5815	-29.3754
25	4.6279	5.5769	4.1723	7.0408	4.0888	6.2032	0.0652	-0.3986	0.1414	0.3885	-0.1316	0.3811	-0.1672	0.1887	0.0832	0.2645	0.0273	0.015	0.3682	-0.0121	0.2273	-73.4466	14.7578	-20.1455
26	4.3711	1.3209	-1.531	1.461	-0.5785	2.2262	-0.0927	-0.1762	-0.3022	0.047	-0.0282	-0.0739	0.168	0.3011	0.1246	0.1598	0.0266	-0.0031	0.1809	0.0207	0.1169	-64.7927	9.6752	-35.8418
27	6.2079	1.7126	-0.5171	1.1918	0.3375	2.399	-0.062	-0.1021	-0.3075	0.0495	-0.0111	0.0012	0.1062	0.0117	0.0728	0.1714	0.0359	0.0055	0.1242	0.0334	0.132	-74.0921	11.0187	-32.7471
28	3.1568	0.6451	-1.2796	0.6667	-0.6531	0.8356	-0.083	-0.0526	-0.014	0.0241	0.0489	0.0008	-0.0373	-0.0012	0.0461	0.1594	0.0121	0.0033	0.1688	-0.014	0.108	-72.2346	15.4435	-34.6226
29	0.3604	-0.4403	1.1614	1.6248	-2.8076	5.5329	-0.0108	0.6035	-0.0333	-0.3553	0.0301	0.1008	0.5515	-0.9254	-0.0385	0.2551	-0.023	-0.0319	0.5466	-0.0246	0.2172	-86.9018	13.8628	-53.1573

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 32 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 44 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 45 through 66 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 80 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 81 through 110 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 111 through 117 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 118 through 165 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 12 through 32 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 33 through 44 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 45 through 66 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 67 through 80 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 81 through 110 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 111 through 151 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 152 through 165 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 12 through 32 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 33 through 44 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 45 through 66 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 67 through 80 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 81 through 110 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 111 through 151 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 152 through 165 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 13 through 32 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 33 through 44 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 45 through 66 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 67 through 80 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 81 through 110 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 111 through 131 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 132 through 151 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 152 through 165 )

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