PDB-6hai: AlbAM131A mutant in complex with albicidin , albicidin resistance...

ID or keywords:

Entry

Database: PDB / ID: 6hai

Title

AlbAM131A mutant in complex with albicidin , albicidin resistance protein

Components

Albicidin resistance protein

Keywords

albicidin binding protein / albicidin resistance protein

Function / homology

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

Function and homology information

Biological species

Klebsiella oxytoca (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.2 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 7, 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 Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
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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PDBx/mmCIF format	6hai.cif.gz	197.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6hai.ent.gz	160.4 KB	Display	PDB format
PDBx/mmJSON format	6hai.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/ha/6hai ftp://data.pdbj.org/pub/pdb/validation_reports/ha/6hai	HTTPS FTP

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Related structure data

Related structure data	6h95C 6h96C 6h97C C: citing same article (ref.)
Similar structure data	6h96-1 6ng9-d 5v3q-d 6m1b-1 6pno-d 4yav-d 4r5q-d 3qav-d 1jj4-d 1xio-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

54.7 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
27.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Albicidin resistance protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.260, 123.497, 161.171
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-442- HOH

#1: Protein	Albicidin resistance protein Mass: 26421.801 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-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-FWW / 4-[[4-[[4-[(3~{S})-3-[[4-[[(~{E})-3-(4-hydroxyphenyl)-2-methyl-prop-2-enoyl]amino]phenyl]carbonylamino]-2,5-bis(oxidanylidene)pyrrolidin-1-yl]phenyl]carbonylamino]-3-methoxy-2-oxidanyl-phenyl]carbonylamino]-3-methoxy-2-oxidanyl-benzoic acid Mass: 843.790 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄₄H₃₇N₅O₁₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.51 Å³/Da / Density % sol: 50.95 %
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: ID23-1 / Wavelength: 0.87313 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 3, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 2.2→49.01 Å / Num. obs: 27360 / % possible obs: 99.45 % / Redundancy: 2 % / R_merge(I) obs: 0.04705 / Net I/σ(I): 7.79
Reflection shell	Resolution: 2.2→2.279 Å / R_merge(I) obs: 0.3389

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Processing

Software

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

Refinement

Resolution: 2.2→49.014 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2399	1387	5.07 %
R_work	0.2105	-	-
obs	0.2121	27333	99.46 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→49.014 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3537	0	134	92	3763

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3769
X-RAY DIFFRACTION	f_angle_d	0.526	5112
X-RAY DIFFRACTION	f_dihedral_angle_d	15.553	2230
X-RAY DIFFRACTION	f_chiral_restr	0.033	501
X-RAY DIFFRACTION	f_plane_restr	0.003	679

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 (%)
2.2-2.2786	0.36	138	0.3109	2524	X-RAY DIFFRACTION	99
2.2786-2.3699	0.3355	119	0.2949	2593	X-RAY DIFFRACTION	100
2.3699-2.4777	0.3474	134	0.2849	2569	X-RAY DIFFRACTION	99
2.4777-2.6083	0.3038	123	0.2623	2555	X-RAY DIFFRACTION	99
2.6083-2.7717	0.2934	154	0.2645	2552	X-RAY DIFFRACTION	99
2.7717-2.9857	0.3014	138	0.2515	2582	X-RAY DIFFRACTION	100
2.9857-3.2861	0.2659	149	0.2204	2580	X-RAY DIFFRACTION	100
3.2861-3.7615	0.2046	143	0.1861	2619	X-RAY DIFFRACTION	100
3.7615-4.7385	0.1883	122	0.1572	2648	X-RAY DIFFRACTION	100
4.7385-49.026	0.2014	167	0.1875	2724	X-RAY DIFFRACTION	99

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	7.3441	0.8333	1.4699	2.1948	-2.4403	5.7925	0.8057	0.8443	1.0079	0.4678	-0.5115	1.6501	-0.9182	-0.8321	-0.1496	0.6723	0.2215	0.136	0.6614	-0.0191	0.7287	-21.9262	100.7023	59.5059
2	2.7532	3.5052	-3.8724	8.2174	-4.9269	5.544	0.9117	2.8619	0.231	-3.6632	-0.8492	1.5154	-0.3084	-2.4039	0.5536	1.2221	0.7355	0.1175	1.1696	0.0196	0.9493	-21.732	99.4642	47.5333
3	9.1527	-4.179	0.9518	3.2028	-2.1369	6.2847	-0.0449	0.011	0.2817	-0.4791	-0.3069	1.0774	-0.319	-1.024	0.4076	0.424	0.0196	-0.0519	0.6743	-0.1551	0.5346	-17.801	85.0651	43.4778
4	3.0237	-0.6967	-1.0112	2.2904	3.2165	9.2384	0.1729	0.429	-0.0964	-0.7705	-0.2169	0.174	-0.1086	-0.1874	0.0017	0.259	-0.0048	-0.0087	0.3965	-0.0286	0.3387	-8.3658	83.9525	44.784
5	3.0683	-1.5347	-2.7188	4.8513	2.0583	7.852	-0.0069	-0.0624	0.0906	0.572	-0.3109	1.3719	0.2633	-0.9766	0.2331	0.3149	0.0509	0.0342	0.5374	-0.0439	0.5267	-17.428	91.0822	58.1933
6	5.2119	-0.288	1.679	1.7303	-0.1217	4.0681	0.1018	0.2479	-0.3719	-0.0157	-0.068	-0.0826	0.3739	0.2551	0.0002	0.3047	0.0292	0.0215	0.2571	-0.0054	0.2852	2.8388	80.3534	53.0221
7	6.5202	3.7334	2.6299	3.6708	2.9644	4.8729	-0.3297	0.0893	0.5031	0.1267	0.1501	0.1047	-0.7917	-0.2754	0.3034	0.3626	0.0203	-0.0393	0.3391	0.019	0.2998	-0.1282	101.2081	63.9427
8	0.8803	0.6916	0.099	4.2087	4.2424	6.7549	-0.0028	0.052	0.0803	0.6078	-0.0449	-0.2336	0.2993	0.0362	0.0647	0.3386	-0.006	-0.029	0.3719	0.0095	0.297	7.0114	93.1228	65.7489
9	8.5485	1.9423	1.4851	8.5845	-4.3545	3.4722	-0.4885	-0.115	0.564	0.0983	-0.3949	-1.2479	-0.581	0.9006	0.8043	0.3704	-0.0768	-0.008	0.6098	-0.0182	0.5515	15.3065	89.0595	54.4202
10	4.5252	-4.3317	-4.3248	7.0191	1.1118	7.7009	0.1429	-0.3787	0.3459	0.2104	0.0814	-0.361	-0.7558	0.9522	-0.1178	0.5115	-0.0248	-0.0243	0.4903	0.0667	0.3701	1.4695	94.3623	50.1037
11	5.058	4.6013	3.6635	7.6393	1.175	5.1046	-0.16	0.5627	0.4738	-0.7226	-0.0539	-0.1377	-0.4282	0.726	0.1067	0.4679	-0.0263	0.0809	0.3231	-0.0091	0.3732	9.3135	102.4965	60.5914
12	6.7521	-0.0006	-2.7194	7.1183	-2.6373	6.6624	0.1071	0.6648	-0.4273	-1.3565	-0.4424	-0.7591	1.031	0.6392	0.4402	0.7278	0.1162	0.2281	0.5066	0.0276	0.6086	8.3247	55.7452	61.5991
13	8.2191	-5.2819	5.5624	9.6053	-6.6476	5.9492	0.325	0.1744	-0.6449	-1.0489	0.0561	-0.354	0.8605	-0.3047	-0.4479	0.6307	0.0151	-0.0265	0.5329	-0.1898	0.5103	-11.1784	57.8656	56.7979
14	3.1141	-4.3568	2.6339	7.9554	-5.1194	7.5523	0.0142	0.0153	-0.5248	-0.0808	0.0102	0.8336	0.4986	-0.7031	-0.1298	0.4843	-0.0246	0.0375	0.4373	-0.0822	0.5436	-14.4701	65.3896	63.1873
15	7.2219	0.2319	1.0938	6.5146	-0.9993	1.0558	-0.2591	0.6575	-0.2436	-1.0911	0.0376	-0.4929	0.0231	0.3	0.1839	0.5587	0.0446	0.1363	0.3849	-0.0084	0.4219	3.0831	64.4498	59.1121
16	5.4775	-3.7825	-2.7253	6.3996	2.9725	3.6297	-0.1445	0.129	0.0463	0.2331	-0.0834	0.2719	0.1388	-0.4324	0.2029	0.3824	0.0469	-0.002	0.2889	-0.0459	0.3798	-13.3271	73.1482	65.7409
17	7.2696	3.1708	-4.3599	6.0325	-1.6669	6.8746	0.2015	0.5445	0.78	-0.2543	0.0852	0.9002	-0.4271	-0.6917	-0.358	0.4259	0.0828	0.0009	0.3558	0.0302	0.4181	-14.1383	84.0032	72.2085
18	5.1847	-4.9088	4.9498	5.4794	-4.9573	5.6458	0.2882	0.3127	0.2782	-0.2715	-0.4576	-0.4919	0.3807	0.4262	0.2025	0.4685	0.0083	0.0234	0.3852	0.0427	0.3836	4.78	72.1724	74.8901
19	7.1341	1.7898	-4.5504	2.332	1.964	8.2626	-0.1425	-0.4429	0.1131	0.8388	0.113	-1.1253	0.2165	0.1538	-0.0335	0.7669	-0.1201	-0.3688	0.5178	0.1645	0.797	11.9606	73.0792	86.7955
20	4.8109	-5.7739	3.4452	8.687	-5.1955	3.9022	-0.3372	0.0161	0.4977	0.5284	-0.0583	-0.6802	-0.6639	0.2811	0.5178	0.4371	-0.0891	-0.0028	0.3089	0.0004	0.314	1.4725	81.8521	78.8455
21	5.4364	5.691	-4.4268	6.7578	-6.2249	6.8933	0.0032	-0.5409	-0.1244	0.4613	-0.2615	-0.0681	0.2348	0.5284	0.3095	0.6745	0.1216	0.0616	0.5204	-0.0854	0.4286	-12.0616	80.5186	83.8163
22	5.3392	-0.2593	4.3053	2.5295	2.3982	4.9397	-0.3616	-0.2986	0.1306	0.3527	0.0852	0.055	-0.2897	0.0888	0.3681	0.5587	-0.0243	0.0619	0.4241	0.0476	0.3409	-2.1094	73.0099	83.1678

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 23 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 24 through 41 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 42 through 65 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 66 through 93 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 94 through 131 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 132 through 154 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 155 through 172 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 173 through 188 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 189 through 199 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 200 through 214 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1 through 22 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 23 through 41 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 42 through 65 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 66 through 93 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 94 through 114 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 115 through 131 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 132 through 147 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 148 through 154 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 155 through 172 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 173 through 188 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 189 through 216 )

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