PDB-6h96: AlbA-albicidin complex, albicidin resistance protein

ID or keywords:

Entry

Database: PDB / ID: 6h96

Title

AlbA-albicidin complex, albicidin resistance protein

Components

Albicidin resistance protein

Keywords

ANTIMICROBIAL PROTEIN / albicidin resistance protein in complex with albicidin

Function / homology

TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / Chem-FWE / Albicidin resistance protein

Function and homology information

Biological species

Klebsiella oxytoca (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Koehnke, J. / Sikandar, A.

Funding support

Germany, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2018
Title: Adaptation of a Bacterial Multidrug Resistance System Revealed by the Structure and Function of AlbA.
Authors: Sikandar, A. / Cirnski, K. / Testolin, G. / Volz, C. / Bronstrup, M. / Kalinina, O.V. / Muller, R. / Koehnke, J.

History

Deposition	Aug 3, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 24, 2019	Group: Data collection / Database references Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2	May 1, 2024	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	6h96.cif.gz	209 KB	Display	PDBx/mmCIF format
PDB format	pdb6h96.ent.gz	168.6 KB	Display	PDB format
PDBx/mmJSON format	6h96.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/h9/6h96 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/6h96	HTTPS FTP

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Related structure data

Related structure data	6h95C 6h97C 6haiC C: citing same article (ref.)
Similar structure data	6hai-1 6pnm-d 1qwg-d 6pno-d 2oo4-1 4r5q-d 6pnn-d 5ueh-d 4is0-d 5yvn-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Albicidin resistance protein

B: Albicidin resistance protein

hetero molecules

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

1

A: Albicidin resistance protein

hetero molecules

defined by author
Evidence: gel filtration
28 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Albicidin resistance protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.142, 123.181, 161.060
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-613- HOH
2	1	A-624- HOH
3	1	B-616- HOH

#1: Protein	Albicidin resistance protein Mass: 27091.553 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: albA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KRS7
#2: Chemical	ChemComp-FWE / 4-[[4-[[4-[(3~{S})-5-azanyl-3-[[4-[[(~{E})-3-(4-hydroxyphenyl)-2-methyl-prop-2-enoyl]amino]phenyl]carbonylamino]-2-oxidanylidene-3~{H}-pyrrol-1-yl]phenyl]carbonylamino]-3-methoxy-2-oxidanyl-phenyl]carbonylamino]-3-methoxy-2-oxidanyl-benzoic acid Mass: 842.806 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄₄H₃₈N₆O₁₂
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.54 Å³/Da / Density % sol: 51.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 0.2-0.4 M Ammonium Sulfate, 0.8-1.2 M Lithium Sulfate, 0.1 M sodium citrate tribasic

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07227 Å / Relative weight: 1
Reflection	Resolution: 1.55→47.37 Å / Num. obs: 77989 / % possible obs: 99.49 % / Redundancy: 2 % / R_merge(I) obs: 0.01922 / Net I/σ(I): 16.72
Reflection shell	Resolution: 1.55→1.605 Å / R_merge(I) obs: 0.3048

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Alba SeMet

Resolution: 1.55→47.37 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.58

	R_factor	Num. reflection	% reflection
R_free	0.2073	3935	5.05 %
R_work	0.1886	-	-
obs	0.1895	77980	99.5 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.55→47.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3552	0	133	442	4127

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3813
X-RAY DIFFRACTION	f_angle_d	0.692	5172
X-RAY DIFFRACTION	f_dihedral_angle_d	14.813	2258
X-RAY DIFFRACTION	f_chiral_restr	0.035	507
X-RAY DIFFRACTION	f_plane_restr	0.005	684

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 (%)
1.55-1.5689	0.2745	124	0.2708	2631	X-RAY DIFFRACTION	100
1.5689-1.5888	0.2429	139	0.255	2621	X-RAY DIFFRACTION	100
1.5888-1.6097	0.2676	134	0.2542	2623	X-RAY DIFFRACTION	100
1.6097-1.6317	0.2683	133	0.2459	2645	X-RAY DIFFRACTION	100
1.6317-1.655	0.2859	131	0.2363	2618	X-RAY DIFFRACTION	100
1.655-1.6797	0.239	171	0.2383	2603	X-RAY DIFFRACTION	100
1.6797-1.706	0.2297	135	0.2379	2622	X-RAY DIFFRACTION	100
1.706-1.734	0.2382	148	0.2356	2637	X-RAY DIFFRACTION	100
1.734-1.7639	0.2652	141	0.2434	2628	X-RAY DIFFRACTION	100
1.7639-1.7959	0.2477	143	0.2272	2589	X-RAY DIFFRACTION	99
1.7959-1.8305	0.2588	118	0.2209	2649	X-RAY DIFFRACTION	99
1.8305-1.8678	0.236	156	0.2197	2650	X-RAY DIFFRACTION	100
1.8678-1.9085	0.2083	143	0.2144	2571	X-RAY DIFFRACTION	100
1.9085-1.9529	0.2863	142	0.2153	2639	X-RAY DIFFRACTION	100
1.9529-2.0017	0.2318	128	0.199	2671	X-RAY DIFFRACTION	100
2.0017-2.0558	0.2021	148	0.1991	2614	X-RAY DIFFRACTION	100
2.0558-2.1163	0.2208	141	0.2	2650	X-RAY DIFFRACTION	100
2.1163-2.1846	0.2086	146	0.1926	2651	X-RAY DIFFRACTION	100
2.1846-2.2627	0.2181	132	0.1829	2664	X-RAY DIFFRACTION	100
2.2627-2.3533	0.1881	138	0.1785	2637	X-RAY DIFFRACTION	100
2.3533-2.4604	0.2139	155	0.1864	2647	X-RAY DIFFRACTION	100
2.4604-2.5901	0.2105	152	0.1817	2653	X-RAY DIFFRACTION	100
2.5901-2.7524	0.1964	131	0.1876	2641	X-RAY DIFFRACTION	99
2.7524-2.9648	0.2148	142	0.1875	2668	X-RAY DIFFRACTION	99
2.9648-3.2631	0.2029	137	0.1876	2668	X-RAY DIFFRACTION	99
3.2631-3.7352	0.1967	135	0.1673	2708	X-RAY DIFFRACTION	99
3.7352-4.7052	0.1592	132	0.1497	2675	X-RAY DIFFRACTION	98
4.7052-47.3951	0.1973	160	0.1875	2772	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	3.8673	-2.7907	-4.2285	4.0229	2.3999	6.2158	0.1938	0.0828	0.3138	-0.1931	-0.0869	-0.3237	-0.7651	0.4567	0.0067	0.1602	-0.0161	-0.025	0.2383	0.0266	0.1707	1.7491	94.1093	50.1404
2	3.24	0.9985	3.4378	6.3623	-0.756	4.342	-0.223	0.3668	0.2639	-0.1254	-0.2116	-0.7465	-0.121	0.7466	0.4455	0.2434	-0.0375	-0.0004	0.3003	0.0579	0.3178	10.088	101.3751	60.4672
3	3.4618	0.8109	-1.0445	2.8868	-1.6899	1.1251	0.0629	0.7948	-0.3704	-1.6935	-0.4922	-0.7653	0.7175	0.4099	0.2925	0.7184	0.2618	0.3002	0.5003	0.1474	0.4574	8.8677	55.7153	61.1215
4	3.152	-1.2947	1.3295	2.0499	-1.2018	3.1014	0.0874	0.1469	-0.3693	-0.2223	0.0173	0.2865	0.6141	-0.1891	-0.1042	0.3171	-0.0557	0.0038	0.175	-0.0221	0.2442	-12.3939	61.8635	60.7054
5	5.7631	-0.3972	-0.2169	2.1203	-0.8757	1.3853	-0.1329	0.546	-0.0445	-1.0002	-0.2271	-0.6199	0.5878	0.4488	0.0986	0.5699	0.0596	0.1545	0.2077	0.0319	0.2754	3.661	64.0572	59.0903
6	0.876	0.2565	-0.4732	3.4854	0.6199	4.0408	-0.0285	0.181	0.1113	0.208	0.0749	0.378	0.1177	-0.4757	-0.0417	0.1386	0.0486	0.0112	0.1919	0.0416	0.2376	-14.1407	77.6309	69.0252
7	1.6468	-0.0152	1.2285	4.1853	-1.694	5.7566	-0.006	0.1689	-0.1132	0.1381	-0.2543	-0.492	0.1293	0.5013	0.2322	0.1598	-0.0245	0.0138	0.1928	0.0538	0.1936	3.9728	77.0224	76.6756
8	3.4501	-0.494	-2.0548	4.111	0.0474	4.7622	0.1188	-0.7331	0.6533	1.1848	0.0934	0.0424	-0.1056	0.887	-0.3648	0.6008	0.0758	0.1933	0.3181	-0.1187	0.2933	-11.2616	80.4853	83.9802
9	6.1531	-1.1794	-2.0972	0.4506	0.1502	2.697	0.3037	-0.1728	0.163	0.5561	-0.1938	0.1973	-0.3509	0.0946	-0.1214	0.3938	-0.0002	0.0646	0.1659	0.0035	0.2257	-6.8489	67.9677	76.8415
10	4.0499	1.4501	1.3136	7.8428	2.5274	5.5293	-0.1955	-0.3298	0.2374	-0.0377	-0.0592	-0.1803	-0.5661	-0.0268	0.266	0.4174	-0.0395	-0.0922	0.2797	0.0425	0.2043	2.4505	77.3809	87.4216
11	4.009	-1.9494	-1.092	4.836	-0.1171	6.1156	0.2967	0.5805	0.0315	-0.15	0.1101	0.9631	-0.4306	-1.1737	-0.2863	0.2491	0.1409	0.0168	0.3706	0.0426	0.412	-21.7112	99.8326	56.088
12	2.6227	-2.4634	0.9306	3.027	-2.3317	3.6464	-0.0129	0.253	-0.001	0.1154	-0.0637	0.3336	-0.104	-0.51	0.0245	0.1514	0.0019	-0.0383	0.3492	-0.039	0.2916	-18.0545	84.9103	43.5531
13	1.9991	-0.8882	-0.4944	5.2368	1.4199	2.7846	-0.0807	0.1126	0.0012	0.0423	0.0843	-0.1118	0.0754	-0.2153	0.0044	0.148	-0.0054	-0.0022	0.2412	-0.0093	0.1644	-8.2477	83.4998	45.0154
14	5.8728	1.9558	-2.5587	2.1407	-2.9962	7.5196	-0.0999	-0.3074	-0.115	0.2404	0.2502	0.2415	-0.082	-0.0171	-0.2206	0.2193	0.1059	-0.0033	0.2417	-0.0291	0.2513	-13.2003	94.925	59.1319
15	-0.0009	-0.0788	-0.1656	1.0074	1.9606	3.8233	0.2004	0.1037	-0.3216	0.379	-0.5664	1.1844	0.0796	-1.8931	0.4285	0.241	-0.0001	0.049	0.718	0.0023	0.5149	-23.1898	84.399	56.9321
16	0.8404	0.3579	0.6323	0.8435	-0.0772	1.7053	-0.0198	0.0434	-0.0001	-0.0062	-0.0698	0.0374	0.0532	0.1174	0.0965	0.1329	0.008	0.0034	0.1875	0.0074	0.1566	1.4484	84.7913	55.5831
17	1.8083	0.0963	1.033	5.6741	0.137	2.3647	-0.1629	-0.1295	0.2551	0.1824	-0.0962	-0.0399	-0.4648	0.0636	0.2197	0.2147	-0.0295	-0.0675	0.1727	-0.0079	0.1665	6.9559	97.3032	66.1063
18	4.6805	-0.3281	1.4401	4.6119	-2.9054	6.1667	-0.2248	-0.2376	0.4491	0.2894	-0.0044	-0.2929	-0.4346	0.6655	0.1813	0.1407	-0.0402	-0.0389	0.4322	-0.0058	0.278	15.4448	88.463	54.2174

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 189 through 199 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 200 through 214 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 22 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 23 through 65 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 66 through 93 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 94 through 127 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 128 through 172 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 173 through 188 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 189 through 199 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 200 through 216 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 2 through 22 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 23 through 41 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 42 through 65 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 66 through 81 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 82 through 93 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 94 through 147 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 148 through 172 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 173 through 188 )

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