PDB-5ne3: L2 class A serine-beta-lactamase complexed with avibactam

ID or keywords:

Entry

Database: PDB / ID: 5ne3

Title

L2 class A serine-beta-lactamase complexed with avibactam

Components

Beta-lactamase

Keywords

Hydrolase/Inhibitor / beta-lactamase / carbapenemase / inhibitor / avibactam / Hydrolase-inhibitor complex

Function / homology

Function and homology information

beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function

Biological species

Stenotrophomonas maltophilia K279a (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.35 Å

Authors

Hinchliffe, P. / Calvopina, K. / Spencer, J.

Citation

Journal: Mol. Microbiol. / Year: 2017
Title: Structural/mechanistic insights into the efficacy of nonclassical beta-lactamase inhibitors against extensively drug resistant Stenotrophomonas maltophilia clinical isolates.
Authors: Calvopina, K. / Hinchliffe, P. / Brem, J. / Heesom, K.J. / Johnson, S. / Cain, R. / Lohans, C.T. / Fishwick, C.W.G. / Schofield, C.J. / Spencer, J. / Avison, M.B.

History

Deposition	Mar 9, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 13, 2017	Provider: repository / Type: Initial release
Revision 2.0	Sep 20, 2017	Group: Advisory / Atomic model / Database references Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / pdbx_validate_close_contact Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.dist
Revision 2.1	Nov 1, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ne3.cif.gz	227.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5ne3.ent.gz	181.1 KB	Display	PDB format
PDBx/mmJSON format	5ne3.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/ne/5ne3 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/5ne3	HTTPS FTP

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Related structure data

Related structure data	5ne1C 5ne2SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6qw7-2 5ul8-d 4uaa-2 4nwm-1 5p9h-d 3g35-2 5eec-2 6nzm-1 3bfe-2 7a61-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 - 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	#164 - Aug 2013 Serotonin Receptor similarity (5) #220 - Apr 2018 Dehalogenases similarity (2) #29 - May 2002 Penicillin-binding Proteins similarity (3) #111 - Mar 2009 Hydrogenase similarity (2) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.492, 84.305, 93.668
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Beta-lactamase / L2 class A serine-beta-lactamase Mass: 29318.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia K279a (bacteria) Gene: Smlt3722 / Plasmid: pOPIN-F / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): SoluBL21 / References: UniProt: B2FRP5, beta-lactamase
#2: Chemical	ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form Mass: 267.260 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C₇H₁₃N₃O₆S / Comment: antibiotic, inhibitor*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.67 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: Crystal reagent (1.5 uL): 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M DL-Glutamic acid; 0.02 M DL-Alanine; 0.02 M Glycine; 0.02 M DL-Lysine; 0.02 M DL-Serine, 0.1 M bicine/Trizma base pH ...Details: Crystal reagent (1.5 uL): 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M DL-Glutamic acid; 0.02 M DL-Alanine; 0.02 M Glycine; 0.02 M DL-Lysine; 0.02 M DL-Serine, 0.1 M bicine/Trizma base pH 8.5 Protein (1 uL): 42 mg/ml, 50 mM Tris pH 7.5, 150 mM NaCl, 5 mM imidazole, 1 mM TCEP

Crystal

Density Matthews: 2.4 Å³/Da / Density % sol: 48.67 %

Crystal grow

Temperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: Crystal reagent (1.5 uL): 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M DL-Glutamic acid; 0.02 M DL-Alanine; 0.02 M Glycine; 0.02 M DL-Lysine; 0.02 M DL-Serine, 0.1 M bicine/Trizma base pH ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 5, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.35→53.623 Å / Num. obs: 116868 / % possible obs: 96.8 % / Redundancy: 11.5 % / CC_1/2: 0.998 / R_pim(I) all: 0.053 / Net I/σ(I): 9.8
Reflection shell	Resolution: 1.35→1.37 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1.3 / CC_1/2: 0.616 / R_pim(I) all: 0.806 / % possible all: 94.2

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5NE2

5ne2

Resolution: 1.35→53.623 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1781	5898	5.05 %
R_work	0.1618	-	-
obs	0.1626	116868	96.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.35→53.623 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4036	0	0	644	4680

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4138
X-RAY DIFFRACTION	f_angle_d	1.349	5634
X-RAY DIFFRACTION	f_dihedral_angle_d	14.155	1518
X-RAY DIFFRACTION	f_chiral_restr	0.082	652
X-RAY DIFFRACTION	f_plane_restr	0.006	748

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 (%)
1.3501-1.3654	0.3522	201	0.3096	3531	X-RAY DIFFRACTION	93
1.3654-1.3815	0.3082	196	0.2901	3582	X-RAY DIFFRACTION	94
1.3815-1.3984	0.2814	184	0.2624	3583	X-RAY DIFFRACTION	94
1.3984-1.4161	0.243	175	0.241	3583	X-RAY DIFFRACTION	94
1.4161-1.4347	0.2495	198	0.2359	3594	X-RAY DIFFRACTION	95
1.4347-1.4544	0.2579	192	0.2322	3587	X-RAY DIFFRACTION	95
1.4544-1.4751	0.2577	174	0.2248	3633	X-RAY DIFFRACTION	95
1.4751-1.4972	0.2264	217	0.2078	3584	X-RAY DIFFRACTION	95
1.4972-1.5206	0.2237	200	0.2006	3604	X-RAY DIFFRACTION	95
1.5206-1.5455	0.2355	166	0.1973	3634	X-RAY DIFFRACTION	95
1.5455-1.5721	0.2009	224	0.1881	3615	X-RAY DIFFRACTION	96
1.5721-1.6007	0.2086	184	0.1817	3665	X-RAY DIFFRACTION	96
1.6007-1.6315	0.1879	196	0.1749	3661	X-RAY DIFFRACTION	96
1.6315-1.6648	0.1919	206	0.1709	3636	X-RAY DIFFRACTION	96
1.6648-1.701	0.181	196	0.1714	3660	X-RAY DIFFRACTION	96
1.701-1.7406	0.1978	212	0.167	3678	X-RAY DIFFRACTION	97
1.7406-1.7841	0.1812	235	0.165	3652	X-RAY DIFFRACTION	97
1.7841-1.8324	0.1823	198	0.162	3698	X-RAY DIFFRACTION	97
1.8324-1.8863	0.176	194	0.1568	3707	X-RAY DIFFRACTION	97
1.8863-1.9472	0.1691	184	0.1498	3727	X-RAY DIFFRACTION	97
1.9472-2.0168	0.1876	189	0.151	3735	X-RAY DIFFRACTION	97
2.0168-2.0975	0.1561	194	0.1471	3740	X-RAY DIFFRACTION	97
2.0975-2.193	0.1687	233	0.1457	3740	X-RAY DIFFRACTION	98
2.193-2.3086	0.1605	189	0.1554	3769	X-RAY DIFFRACTION	98
2.3086-2.4532	0.1526	187	0.1509	3794	X-RAY DIFFRACTION	99
2.4532-2.6427	0.164	192	0.1492	3847	X-RAY DIFFRACTION	98
2.6427-2.9086	0.1883	195	0.1525	3817	X-RAY DIFFRACTION	98
2.9086-3.3294	0.153	194	0.1462	3886	X-RAY DIFFRACTION	99
3.3294-4.1945	0.1399	187	0.1355	3940	X-RAY DIFFRACTION	99
4.1945-53.6655	0.1698	206	0.1553	4088	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	1.1013	-0.0205	0.1131	0.8379	-0.02	0.527	0.0421	0.0436	0.0081	0.0044	-0.0165	0.1457	-0.0395	-0.0784	-0.023	0.1039	0.0142	0.0194	0.1421	0.0038	0.1377	142.3914	173.6367	286.857
2	1.3614	-0.4698	-0.39	0.9082	0.1318	0.5702	-0.035	-0.1581	0.0054	0.1175	0.0341	-0.0252	0.0004	0.0641	-0.0012	0.14	0.0002	-0.0111	0.1479	0.009	0.1166	166.9957	165.9537	295.1352
3	1.9256	-0.13	-0.8331	1.2266	-0.225	1.6046	-0.0043	-0.1777	0.0288	0.1285	0.0103	0.031	-0.0394	-0.0011	-0.0301	0.1036	0.0074	0.0006	0.0928	-0.0048	0.0698	157.9012	175.0792	294.2106
4	1.8428	0.7997	-0.1245	3.0281	-0.1988	0.8176	0.0324	0.0939	-0.0008	-0.0615	-0.0326	0.0266	-0.0295	-0.0047	-0.0046	0.0753	0.0137	0.0069	0.1013	0.0034	0.0779	152.4025	173.5446	282.3759
5	3.0457	2.3457	-0.7134	3.0064	-2.4886	3.3834	0.0132	0.1798	0.0344	-0.129	0.024	0.1529	-0.049	-0.1282	-0.0309	0.0864	0.0135	-0.0208	0.1653	-0.0038	0.101	144.5205	172.8325	278.4022
6	0.7454	-0.133	0.5092	1.3724	-0.1126	2.6919	0.0907	0.0614	-0.0648	-0.1949	-0.0873	-0.0015	0.4445	0.0843	-0.0169	0.1602	0.0257	0.0145	0.126	0.0019	0.1223	186.015	152.3791	261.3315
7	1.7978	-0.8253	1.1609	3.4865	1.6942	2.5942	0.0618	-0.1316	0.1017	0.1072	0.0987	-0.3706	-0.0833	0.1501	-0.166	0.1028	-0.0284	-0.0014	0.1501	-0.0047	0.1727	187.4436	173.0414	277.432
8	1.3843	-2.4796	0.4544	5.1056	-2.7535	7.3441	-0.0858	-0.0538	0.2165	0.1348	-0.0057	-0.0969	-0.2601	0.2112	0.0959	0.0927	-0.0561	0.0212	0.0911	-0.0119	0.1425	177.8371	182.6498	279.3452
9	3.7382	-3.316	-5.21	3.664	3.9354	8.9443	0.093	0.2272	-0.1616	0.0018	-0.0599	0.2394	0.0974	-0.3389	0.0025	0.0963	-0.0058	-0.0255	0.1472	0.0032	0.1478	167.9705	177.5351	271.2834
10	0.4555	-0.23	-0.1097	1.0376	0.2678	0.8727	0.0192	0.0218	0.008	-0.0714	-0.028	-0.0384	-0.051	0.1097	0.0074	0.0901	-0.0092	-0.0076	0.1322	0.0096	0.132	186.095	171.103	269.1023
11	1.6691	0.904	-1.2538	3.1701	0.9509	2.3166	-0.0211	-0.324	-0.0239	0.1971	0.0215	-0.1703	-0.0827	0.2078	0.0038	0.1222	0.0032	-0.0216	0.1528	0.0151	0.1199	186.1689	164.5715	283.545
12	0.8612	0.0412	0.6374	1.2555	-0.52	2.9065	0.0223	-0.0259	-0.0367	-0.0148	-0.0169	0.0704	0.1375	0.0012	-0.0184	0.0783	0.0042	-0.0037	0.0883	-0.0006	0.1052	179.9507	155.4565	269.9489
13	7.8313	-5.8202	6.2725	7.7667	-6.2107	7.433	-0.005	-0.1025	-0.2442	-0.1537	0.1122	0.1718	0.2317	-0.153	-0.1543	0.1596	-0.0077	-0.0026	0.0967	-0.0147	0.1101	178.4927	148.9081	264.3928

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 through 71 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 72 through 167 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 168 through 212 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 213 through 271 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 272 through 289 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 21 through 71 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 72 through 86 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 87 through 101 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 102 through 115 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 116 through 194 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 195 through 212 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 213 through 271 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 272 through 289 )

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