PDB-4is9: Crystal Structure of the Escherichia coli LpxC/L-161,240 complex

ID or keywords:

Entry

Database: PDB / ID: 4is9

Title

Crystal Structure of the Escherichia coli LpxC/L-161,240 complex

Components

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

Keywords

HYDROLASE/HYDROLASE INHIBITOR / LPXC / DEACETYLATION / ANTIBIOTIC / ACYL UDP-GLCNAC / HYDROXAMATE / L-161 / 240 / BAAB SANDWICH / LIPID A BIOSYNTHESIS / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

lpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta / ISOPROPYL ALCOHOL / Chem-LTF / :

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.13 Å

Authors

Lee, C.-J. / Zhou, P.

Citation

Journal: Acs Chem.Biol. / Year: 2014
Title: Structural Basis of the Promiscuous Inhibitor Susceptibility of Escherichia coli LpxC.
Authors: Lee, C.J. / Liang, X. / Gopalaswamy, R. / Najeeb, J. / Ark, E.D. / Toone, E.J. / Zhou, P.

History

Deposition	Jan 16, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 30, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2014	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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	4is9.cif.gz	258.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4is9.ent.gz	211.8 KB	Display	PDB format
PDBx/mmJSON format	4is9.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/is/4is9 ftp://data.pdbj.org/pub/pdb/validation_reports/is/4is9	HTTPS FTP

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Related structure data

Related structure data	4isaC 4mqyC C: citing same article (ref.)
Similar structure data	1kn9-3 6znd-1 4n2o-10 6ijr-1 3cnz-2 6amw-d 5tzw-4 4d09-3 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
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

hetero molecules

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

1

A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

hetero molecules

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

2

B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	117.440, 117.440, 253.661
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	A-608- HOH
2	1	B-553- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase / UDP-3-O-acyl-GlcNAc deacetylase Mass: 33554.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: IHE3034 / ExPEC / Gene: lpxC, ECOK1_0097 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: D5CV28, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

#1: Protein

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase / UDP-3-O-acyl-GlcNAc deacetylase

Mass: 33554.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: IHE3034 / ExPEC / Gene: lpxC, ECOK1_0097 / Plasmid: PET21B / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D5CV28, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 5 types, 283 molecules

#2: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-LTF / (4R)-2-(3,4-dimethoxy-5-propylphenyl)-N-hydroxy-4,5-dihydro-1,3-oxazole-4-carboxamide Mass: 308.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₀N₂O₅
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 276 / 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: 50.96 %

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-BM / Wavelength: 1 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 17, 2009

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.13→50 Å / Num. obs: 37998 / % possible obs: 100 % / Redundancy: 13.4 % / R_merge(I) obs: 0.086 / Net I/σ(I): 9.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.13-2.17	13.1	0.603	1	100
2.17-2.21	13.7	0.727	1	100
2.21-2.25	11.7	0.673	1	100
2.25-2.29	11.6	0.706	1	100
2.29-2.34	13.8	0.357	1	100
2.34-2.4	13.8	0.274	1	100
2.4-2.46	13.8	0.228	1	100
2.46-2.53	13.8	0.196	1	100
2.53-2.6	13.9	0.16	1	100
2.6-2.68	13.8	0.138	1	100
2.68-2.78	13.9	0.121	1	100
2.78-2.89	13.8	0.096	1	100
2.89-3.02	13.8	0.085	1	100
3.02-3.18	13.8	0.074	1	100
3.18-3.38	13.8	0.066	1	100
3.38-3.64	12.6	0.062	1	100
3.64-4.01	13.2	0.075	1	99.9
4.01-4.59	13.7	0.074	1	100
4.59-5.78	13.6	0.062	1	100
5.78-50	12.7	0.057	1	99.5

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.11	data extraction
MAR345		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.13→35.916 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.62 / σ(F): 1.39 / Phase error: 26.23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2473	1896	4.99 %
R_work	0.2158	-	-
obs	0.2173	37998	99.91 %

Solvent computation

Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.86 Å² / k_sol: 0.355 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.7947 Å²	0 Å²	-0 Å²
2-	-	0.7947 Å²	-0 Å²
3-	-	-	-1.5894 Å²

Refinement step

Cycle: LAST / Resolution: 2.13→35.916 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4705	0	55	276	5036

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4894
X-RAY DIFFRACTION	f_angle_d	0.705	6637
X-RAY DIFFRACTION	f_dihedral_angle_d	12.404	1816
X-RAY DIFFRACTION	f_chiral_restr	0.041	732
X-RAY DIFFRACTION	f_plane_restr	0.003	865

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 (%)
2.13-2.1823	0.3213	115	0.2794	2551	X-RAY DIFFRACTION	100
2.1823-2.2413	0.3578	142	0.2956	2545	X-RAY DIFFRACTION	100
2.2413-2.3072	0.3953	123	0.2996	2589	X-RAY DIFFRACTION	100
2.3072-2.3817	0.3096	138	0.2572	2499	X-RAY DIFFRACTION	100
2.3817-2.4668	0.2765	145	0.249	2576	X-RAY DIFFRACTION	100
2.4668-2.5655	0.3073	128	0.2462	2557	X-RAY DIFFRACTION	100
2.5655-2.6822	0.3018	131	0.2508	2577	X-RAY DIFFRACTION	100
2.6822-2.8236	0.2946	148	0.2547	2537	X-RAY DIFFRACTION	100
2.8236-3.0004	0.2828	131	0.237	2581	X-RAY DIFFRACTION	100
3.0004-3.232	0.2618	140	0.2309	2572	X-RAY DIFFRACTION	100
3.232-3.5569	0.2258	119	0.2133	2603	X-RAY DIFFRACTION	100
3.5569-4.071	0.22	155	0.1895	2585	X-RAY DIFFRACTION	100
4.071-5.1267	0.1941	139	0.167	2628	X-RAY DIFFRACTION	100
5.1267-35.9208	0.2154	142	0.2003	2702	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	2.4192	0.0683	0.5779	1.4633	0.6341	2.2866	-0.2455	1.0575	-0.1044	-0.2596	0.377	0.0467	-0.0103	-0.2652	-0.0942	0.4058	-0.183	-0.0218	0.6699	-0.0408	0.2875	23.4085	8.6908	14.0392
2	2.2148	0.1606	0.3992	2.2101	-0.3112	1.5099	-0.0995	0.332	0.3825	-0.07	0.1217	0.2644	-0.167	-0.071	-0.0019	0.3296	-0.104	-0.0738	0.3421	0.0241	0.3706	23.8773	23.7669	27.9545
3	2.3059	-0.9127	0.8085	3.3279	-0.1197	1.647	0.1848	-0.3478	0.1014	0.1183	0.0259	0.022	0.4329	0.2122	-0.0841	0.4351	-0.0966	-0.0563	0.2883	0.0284	0.2659	24.295	12.1251	39.2547
4	2.1733	0.5351	1.0089	2.4604	0.7843	2.3446	0.1565	-0.028	-0.3631	0.0577	0.0533	-0.093	0.3137	0.014	-0.1661	0.305	-0.0574	-0.0245	0.2931	0.0079	0.349	24.0481	3.6009	32.3444
5	1.7085	1.1295	-0.6009	1.0626	-0.183	0.9857	-0.0832	0.3773	0.602	0.0583	0.0825	0.0952	-0.365	0.0981	-0.0539	0.3585	-0.1229	-0.1248	0.4407	0.1866	0.5668	26.871	31.6857	22.4329
6	2.5314	-0.7188	0.1893	2.1845	1.0367	0.6037	-0.213	-1.5261	-0.2403	0.5747	0.1724	0.2925	0.6126	0.078	-0.0914	0.6031	0.0543	0.0155	0.8975	0.055	0.3177	49.3106	-2.4929	31.0744
7	0.42	0.1999	0.1249	1.0981	-0.3101	0.1785	-0.2925	-0.5488	-0.6296	0.6303	0.2973	-0.3039	0.8953	0.3613	-0.1006	1.031	0.3889	-0.1049	1.1893	0.2083	0.6651	58.4225	-12.3215	31.9558
8	4.797	-0.3866	-0.076	2.9744	-2.4403	2.0396	-0.452	-0.1489	-1.5486	0.7598	0.1247	-0.3821	1.3408	0.5444	-0.0661	1.1357	0.4256	0.143	0.7932	0.1158	0.9315	57.8672	-17.8452	26.3308
9	2.3871	-1.4316	-0.9782	2.053	0.7587	2.4348	-0.1722	-0.5029	-0.6134	0.6399	0.0219	0.2215	0.536	0.5845	0.1583	0.4741	0.0477	0.0208	0.6057	-0.0208	0.4424	48.2644	-4.6322	25.3195
10	2.0195	0.5039	-0.1071	0.9698	-0.8346	1.0524	-0.0257	-0.1225	-0.4254	-0.3098	-0.0593	-0.1171	-0.0329	0.0485	0.0782	0.3582	0.1361	-0.0727	0.5711	-0.2329	0.482	64.8782	0.2207	14.3367
11	2.2211	1.4545	0.9445	2.6833	0.2447	1.7519	-0.0707	0.3812	0.1276	-0.4762	-0.0151	0.1994	0.1028	-0.3523	0.1906	0.4621	0.0054	-0.0911	0.6244	-0.2651	0.4837	53.6302	-7.1344	2.333
12	0.405	1.0839	-0.2816	3.4467	-0.2168	0.9226	0.201	0.2386	0.2221	-0.1231	-0.035	0.876	-0.2392	-0.0911	-0.0044	0.2316	0.0856	0.0263	0.609	-0.1762	0.4077	48.3734	0.3125	10.3218
13	0.4236	-0.3948	-0.3132	0.4104	0.3662	0.4008	-0.5773	0.1468	-0.4679	-0.0873	0.4541	-1.0402	1.0924	0.0862	-0.2645	0.9479	-0.1303	0.3189	0.5912	-0.3608	1.2738	41.958	-23.5748	14.6995
14	1.4413	0.2525	0.0531	1.3981	-0.6662	2.0299	-0.2611	0.2126	-0.6953	-0.1852	0.1072	0.2129	0.4159	-0.4454	0.1006	0.3877	0.0108	-0.0181	0.6185	-0.2851	0.611	50.1342	-8.0971	9.6223
15	0.8114	-0.1183	-1.1671	1.1322	-0.3474	2.9222	-0.3123	-0.2231	-0.6411	-0.1505	0.094	-0.0357	0.7237	0.76	0.1604	0.3367	0.1818	-0.0368	0.5262	-0.1826	0.5951	69.855	-3.82	15.9935
16	0.2741	0.2475	-1.0962	0.4019	-0.7577	4.7181	0.737	-0.0949	0.8589	-0.1898	0.1845	-0.0848	-0.673	-0.1579	0.385	0.3579	0.1203	-0.0224	0.477	-0.2744	1.0574	71.325	20.7533	24.5663

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 1:118)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 119:148)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 149:167)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 168:264)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 265:300)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 1:36)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 37:59)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 60:77)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 78:118)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 119:148)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 149:171)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 172:191)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 192:218)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 219:264)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 265:285)
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESSEQ 286:299)

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Assembly

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Components

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 283 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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