PDB-5ixh: Crystal Structure of Burkholderia cenocepacia BcnA

ID or keywords:

Entry

Database: PDB / ID: 5ixh

Title

Crystal Structure of Burkholderia cenocepacia BcnA

Components

YceI-like domain protein

Keywords

UNKNOWN FUNCTION / beta barrel lipocalin

Function / homology

Chem-OTP / :

Function and homology information

Biological species

Burkholderia cenocepacia BC7 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Loutet, S.A. / Murphy, M.E.P.

Citation

Journal: MBio / Year: 2017
Title: Antibiotic Capture by Bacterial Lipocalins Uncovers an Extracellular Mechanism of Intrinsic Antibiotic Resistance.
Authors: El-Halfawy, O.M. / Klett, J. / Ingram, R.J. / Loutet, S.A. / Murphy, M.E. / Martin-Santamaria, S. / Valvano, M.A.

History

Deposition	Mar 23, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 29, 2017	Group: Database references
Revision 1.2	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ixh.cif.gz	214.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5ixh.ent.gz	177.7 KB	Display	PDB format
PDBx/mmJSON format	5ixh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ixh_validation.pdf.gz	717.1 KB	Display	wwPDB validaton report
Full document	5ixh_full_validation.pdf.gz	726.4 KB	Display
Data in XML	5ixh_validation.xml.gz	18.9 KB	Display
Data in CIF	5ixh_validation.cif.gz	26.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ix/5ixh ftp://data.pdbj.org/pub/pdb/validation_reports/ix/5ixh	HTTPS FTP

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Related structure data

Related structure data	5ixgC 2fgsS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4w52-d 3zc4-9 5jgz-d 2ray-d 210l-d 6uxc-1 4w56-d 2w2s-d 7lzm-d 3zc4-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: YceI-like domain protein

B: YceI-like domain protein

hetero molecules

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

1

A: YceI-like domain protein

hetero molecules

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

2

B: YceI-like domain protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	93.970, 93.970, 76.660
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	YceI-like domain protein Mass: 17169.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia BC7 (bacteria) Gene: BURCENBC7_AP5370 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U1XQX6
#2: Chemical	ChemComp-OTP / (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE / OCTAPRENYL PYROPHOSPHATE Mass: 722.911 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄₀H₆₈O₇P₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.85 Å³/Da / Density % sol: 56.77 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris, ammonium sulphate

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.97949 Å

Detector

Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 15, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 1.4→35.94 Å / Num. obs: 75559 / % possible obs: 99.9 % / Redundancy: 10.5 % / B_iso Wilson estimate: 15.82 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.063 / R_pim(I) all: 0.02 / R_rim(I) all: 0.066 / Net I/σ(I): 17.1 / Num. measured all: 796780 / Scaling rejects: 119

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.4-1.43	5.7	0.545	1	99.4
7.41-35.94	10.1	0.041	1	93.2

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
Aimless	0.1.26	data scaling
PHASER		phasing
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2FGS

2fgs

Resolution: 1.4→34.676 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.98

	R_factor	Num. reflection	% reflection
R_free	0.1832	3800	5.04 %
R_work	0.1563	-	-
obs	0.1577	75461	99.82 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 224.37 Å² / B_iso mean: 31.6793 Å² / B_iso min: 9.71 Å²

Refinement step

Cycle: final / Resolution: 1.4→34.676 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2396	0	288	274	2958
B_iso mean	-	-	67.84	35.76	-
Num. residues	-	-	-	-	320

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2640
X-RAY DIFFRACTION	f_angle_d	1.464	3593
X-RAY DIFFRACTION	f_chiral_restr	0.077	400
X-RAY DIFFRACTION	f_plane_restr	0.006	460
X-RAY DIFFRACTION	f_dihedral_angle_d	14.941	965

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.4-1.4178	0.2732	125	0.2467	2652	2777	99
1.4178-1.4364	0.2522	134	0.2226	2645	2779	99
1.4364-1.4561	0.2171	131	0.2079	2597	2728	100
1.4561-1.4769	0.2129	134	0.1988	2687	2821	100
1.4769-1.4989	0.2323	140	0.1925	2674	2814	100
1.4989-1.5224	0.2335	140	0.1849	2617	2757	100
1.5224-1.5473	0.2064	134	0.1781	2649	2783	100
1.5473-1.574	0.1978	151	0.1735	2643	2794	100
1.574-1.6026	0.2142	134	0.171	2645	2779	100
1.6026-1.6334	0.199	110	0.1757	2682	2792	100
1.6334-1.6668	0.1952	150	0.1651	2661	2811	100
1.6668-1.703	0.2017	154	0.1757	2613	2767	100
1.703-1.7426	0.1942	146	0.1672	2662	2808	100
1.7426-1.7862	0.2054	160	0.1575	2617	2777	100
1.7862-1.8345	0.1801	136	0.1604	2675	2811	100
1.8345-1.8885	0.1775	156	0.151	2635	2791	100
1.8885-1.9494	0.1727	152	0.1535	2612	2764	100
1.9494-2.0191	0.1542	143	0.1461	2688	2831	100
2.0191-2.0999	0.1753	122	0.1433	2652	2774	100
2.0999-2.1955	0.1731	148	0.1455	2667	2815	100
2.1955-2.3112	0.1729	120	0.1418	2665	2785	100
2.3112-2.456	0.1883	161	0.1536	2662	2823	100
2.456-2.6456	0.1695	147	0.1546	2667	2814	100
2.6456-2.9117	0.1899	139	0.1538	2661	2800	100
2.9117-3.3327	0.1859	156	0.1619	2676	2832	100
3.3327-4.1977	0.1645	144	0.1344	2675	2819	100
4.1977-34.6869	0.1814	133	0.157	2682	2815	98

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	1.6435	0.9249	0.1682	0.8702	-0.6904	2.6235	0.0535	0.5554	-0.3362	-1.0392	0.0086	-0.3041	-0.2404	0.6705	-1.3134	0.4468	-0.1404	0.0826	0.2859	-0.0694	0.1033	65.723	0.4356	73.9581
2	2.6905	-1.4282	-1.4189	4.5844	4.7071	7.3336	0.116	0.0441	0.0712	-0.5567	-0.0034	-0.1656	-0.7007	0.0639	0.1853	0.2585	-0.0406	0.0361	0.0746	0.029	0.114	56.8466	5.0824	76.0824
3	2.8658	2.7693	5.2014	2.7226	5.0719	9.6115	0.0539	-0.429	0.6223	0.2574	-0.0899	0.2244	-0.2616	-0.1078	-0.0554	0.3218	-0.0168	0.0212	0.2233	-0.0838	0.2756	52.1606	15.1241	93.3425
4	1.7921	-1.8575	-2.2244	2.481	2.1109	2.6888	0.0363	0.0739	0.1011	-0.0398	0.0666	-0.2009	-0.096	-0.0991	0.1353	0.2195	-0.0091	0.0071	0.1207	-0.0076	0.1013	52.7332	0.6261	75.4753
5	6.6734	-1.2489	-4.0801	5.9541	3.271	7.7379	-0.0277	0.3992	-0.4239	-0.6625	0.1898	-0.6266	-0.0891	0.2035	-0.1089	0.192	-0.0084	0.0663	0.16	-0.0716	0.2127	63.7974	-9.6167	64.4591
6	3.6424	-4.7488	-1.2915	6.94	0.6544	4.7194	0.174	0.1618	-0.2076	-0.1662	-0.1438	-0.1934	0.3038	0.0405	-0.0525	0.1624	-0.006	-0.0149	0.1095	-0.0092	0.1347	54.0545	-13.9766	71.0116
7	0.998	0.5077	0.645	1.7388	1.1851	2.7532	0.0194	-0.0798	0.1117	-0.0494	-0.0159	-0.0085	-0.2415	0.0297	0.0159	0.1657	-0.0115	0.0036	0.1015	-0.0062	0.0934	55.3048	4.6424	87.8223
8	3.6102	3.8433	3.2566	3.6747	3.6185	6.2002	0.1603	-0.0845	0.0517	0.2223	-0.1011	0.0268	0.1512	-0.0535	-0.0338	0.1013	0.0194	-0.0114	0.0747	-0	0.0964	55.9741	-0.7987	86.6333
9	3.122	3.1131	0.5925	5.8206	-2.5348	2.8096	0.0485	-0.014	0.0964	0.2733	-0.1015	-0.0256	-0.2746	0.212	0.0091	0.1396	-0.0093	0.0433	0.0975	-0.0424	0.0842	59.3579	6.0066	85.9747
10	0.8109	0.5359	0.7679	1.7293	-0.1712	1.378	0.0157	-0.0431	0.0809	0.1647	-0.0146	-0.0136	-0.2352	0.2065	-0.0363	0.1709	-0.0145	0.017	0.1293	-0.0214	0.1068	61.7309	-0.331	82.4755
11	5.1678	-0.6606	0.7922	5.7198	0.0512	2.2907	0.054	0.2653	-0.4163	-0.1176	0.1511	-0.3773	0.8087	0.5874	-0.1628	0.2619	0.0937	-0.0053	0.2177	-0.0377	0.1945	64.901	-18.9493	76.9186
12	3.9801	-4.8763	0.6297	7.496	-1.4357	0.4127	-0.3008	0.0663	-0.0493	-0.3739	0.4101	-0.4031	-0.3001	0.2889	0.0718	0.3988	-0.0629	-0.0102	0.1712	-0.0446	0.1372	63.0097	3.88	78.9863
13	3.4649	3.5413	0.7043	8.5413	1.7258	4.7541	0.067	-0.2295	0.2288	0.2271	-0.2042	0.6069	0.2709	-0.3966	0.0304	0.2734	0.0456	0.0151	0.1481	0.0186	0.1562	30.4798	0.4696	76.6105
14	2.2981	2.1721	3.5107	2.4015	3.1826	7.4021	0.2175	-0.5716	0.4002	0.5353	-0.3273	0.5556	-0.1401	-0.6644	0.1356	0.236	0.0204	0.0566	0.164	0.0089	0.2105	29.5789	-3.7397	81.382
15	1.2106	-0.175	-0.3827	4.3165	-5.1542	7.8037	0.0023	0.0476	0.1763	0.078	-0.0563	-0.0436	-0.2285	0.163	0.2134	0.2319	-0.0166	-0.007	0.1034	-0.0101	0.1471	41.9749	4.9984	69.9064
16	5.2877	-0.6079	-3.0658	3.7684	-0.5296	4.5416	-0.0512	-0.3576	-0.3386	0.2013	0.1293	0.3299	0.0968	-0.0667	-0.0691	0.17	-0.0123	-0.0109	0.1106	0.0423	0.1414	34.2095	-13.6497	84.0766
17	1.3467	-0.5377	0.7361	2.7728	-1.6279	3.0651	-0.0121	0.0797	0.0898	0.1021	-0.0432	-0.0087	-0.243	0.0674	0.055	0.1264	-0.0033	0.0013	0.0738	-0.0097	0.0767	39.018	1.9849	64.7077
18	2.9963	-2.9733	1.3299	3.2903	-0.6565	2.2358	0.0862	0.0853	0.0308	-0.0133	-0.0195	0.0205	-0.0454	-0.0351	-0.0053	0.0998	-0.0223	-0.0082	0.0752	-0.0044	0.0857	37.7989	-2.971	64.8878
19	3.0296	-1.7758	1.1585	1.6513	1.054	2.8773	0.0752	0.0478	0.143	-0.2838	-0.1041	0.0016	-0.2639	-0.1834	-0.0309	0.1194	-0.0017	0.0492	0.0904	0.035	0.0912	34.9849	3.6298	65.6609
20	1.5018	0.8089	0.291	7.1428	-0.0887	1.5313	0.0197	0.0285	-0.1283	0.0959	0.0586	0.1932	0.0897	-0.2681	-0.0354	0.1421	-0.0279	0.0085	0.1608	0.0071	0.0918	29.9222	-10.9007	71.9435
21	6.0827	5.3851	0.147	5.1631	0.8404	2.9373	-0.2458	0.0062	0.088	-0.2882	0.2075	0.1495	-0.2289	-0.0937	0.1593	0.2349	0.0316	-0.0207	0.1402	0.0313	0.1253	30.9297	1.5884	72.5842

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 23 )	A	5 - 23
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 38 )	A	24 - 38
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 45 )	A	39 - 45
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 46 through 55 )	A	46 - 55
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 56 through 67 )	A	56 - 67
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 68 through 79 )	A	68 - 79
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 80 through 94 )	A	80 - 94
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 95 through 106 )	A	95 - 106
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 107 through 122 )	A	107 - 122
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 123 through 137 )	A	123 - 137
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 138 through 152 )	A	138 - 152
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 153 through 163 )	A	153 - 163
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 3 through 22 )	B	3 - 22
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 23 through 30 )	B	23 - 30
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 31 through 55 )	B	31 - 55
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 56 through 79 )	B	56 - 79
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 80 through 94 )	B	80 - 94
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 95 through 106 )	B	95 - 106
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 107 through 122 )	B	107 - 122
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 123 through 152 )	B	123 - 152
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 153 through 163 )	B	153 - 163

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