PDB-5ne1: L2 class A serine-beta-lactamase in complex with cyclic boronate 2

ID or keywords:

Entry

Database: PDB / ID: 5ne1

Title

L2 class A serine-beta-lactamase in complex with cyclic boronate 2

Components

Beta-lactamase

Keywords

HYDROLASE / beta-lactamase / carbapenemase / cyclic boronate / inhibitor

Function / homology

Function and homology information

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

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.09 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 1.1	Sep 20, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.2	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 2.0	Oct 30, 2019	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary Category: chem_comp / entity / pdbx_entity_nonpoly Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1	Jan 17, 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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PDBx/mmCIF format	5ne1.cif.gz	220 KB	Display	PDBx/mmCIF format
PDB format	pdb5ne1.ent.gz	176.5 KB	Display	PDB format
PDBx/mmJSON format	5ne1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ne/5ne1 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/5ne1	HTTPS FTP

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Related structure data

Related structure data	5ne2SC 5ne3C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4yfm-2 6d15-d 4xtz-2 6qw7-1 4opy-d 3g35-2 2ax6-d 5e2e-2 4qe6-d 5ne3-2 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

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

1

A: Beta-lactamase

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

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.380, 85.690, 113.180
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 Mass: 29318.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Gene: blaL2, L2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SoluBL21 / References: UniProt: Q9RBQ1, beta-lactamase
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Chemical	ChemComp-OK3 / (4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid Mass: 357.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₁₈BN₂O₆
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.9 Å³/Da / Density % sol: 57.64 %
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: 2.9 Å³/Da / Density % sol: 57.64 %

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: I04-1 / Wavelength: 0.92819 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 30, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92819 Å / Relative weight: 1
Reflection	Resolution: 2.09→44.1 Å / Num. obs: 40861 / % possible obs: 99.3 % / Redundancy: 13.1 % / CC_1/2: 0.992 / R_pim(I) all: 0.126 / Net I/σ(I): 8
Reflection shell	Resolution: 2.09→2.14 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.4 / CC_1/2: 0.534 / R_pim(I) all: 0.8 / % possible all: 99.5

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5NE2

5ne2

Resolution: 2.09→42.845 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2143	2034	4.98 %
R_work	0.1756	-	-
obs	0.1776	40861	99.13 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.09→42.845 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4018	0	35	325	4378

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4135
X-RAY DIFFRACTION	f_angle_d	1.249	5622
X-RAY DIFFRACTION	f_dihedral_angle_d	14.33	1519
X-RAY DIFFRACTION	f_chiral_restr	0.059	652
X-RAY DIFFRACTION	f_plane_restr	0.005	745

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 (%)
2.09-2.1386	0.2765	136	0.2439	2536	X-RAY DIFFRACTION	99
2.1386-2.1921	0.328	122	0.2507	2556	X-RAY DIFFRACTION	99
2.1921-2.2514	0.3181	139	0.2456	2495	X-RAY DIFFRACTION	98
2.2514-2.3176	0.2715	142	0.2311	2542	X-RAY DIFFRACTION	99
2.3176-2.3924	0.2858	126	0.2059	2564	X-RAY DIFFRACTION	99
2.3924-2.4779	0.2544	128	0.1961	2578	X-RAY DIFFRACTION	100
2.4779-2.5771	0.2156	121	0.1919	2593	X-RAY DIFFRACTION	99
2.5771-2.6944	0.205	143	0.1809	2580	X-RAY DIFFRACTION	100
2.6944-2.8364	0.2541	134	0.178	2600	X-RAY DIFFRACTION	100
2.8364-3.0141	0.2075	135	0.1692	2573	X-RAY DIFFRACTION	100
3.0141-3.2467	0.2086	140	0.1718	2557	X-RAY DIFFRACTION	98
3.2467-3.5733	0.1933	125	0.1563	2632	X-RAY DIFFRACTION	100
3.5733-4.09	0.2063	146	0.1421	2622	X-RAY DIFFRACTION	100
4.09-5.1516	0.1584	141	0.1449	2658	X-RAY DIFFRACTION	99
5.1516-42.854	0.1881	156	0.1766	2741	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	1.6457	0.3096	0.5482	1.1592	0.1879	1.2575	0.0499	-0.0468	0.0602	0.0158	-0.0767	0.2955	0.0171	-0.1462	0.0229	0.1724	0.0228	0.0201	0.1901	0.0064	0.2189	137.3457	91.4552	231.7934
2	3.5126	-0.9675	-0.5598	1.6987	0.0141	0.889	-0.0964	-0.5856	0.2225	0.2101	0.1546	-0.1271	-0.1124	0.0682	-0.0547	0.3031	0.0357	-0.0088	0.3077	-0.0114	0.2054	166.7415	88.084	242.0439
3	6.956	-0.3384	-0.8535	1.3316	-0.219	0.3928	-0.1454	0.0765	-0.3404	0.109	0.0417	0.0616	0.0758	0.1142	0.1038	0.2679	-0.005	-0.0077	0.1847	-0.0169	0.1831	167.1083	71.7612	233.6248
4	0.9997	-0.0476	-0.3078	0.8768	0.3102	0.1915	0.0557	-0.0727	0.0212	0.0497	-0.004	-0.0647	-0.0476	-0.0201	-0.0504	0.2205	0.0184	0.0094	0.1886	0.0125	0.1317	160.5577	84.2241	242.2036
5	2.263	0.0252	-0.6772	3.5849	-0.9276	2.2343	0.0358	-0.1579	-0.0277	0.1188	-0.0993	0.4753	0.135	-0.0034	0.0624	0.2431	0.0308	0.0179	0.2485	-0.003	0.203	148.0215	87.3959	242.8384
6	1.6374	0.0267	0.1006	1.1898	0.0626	0.8144	0.0867	0.1184	0.0445	0.012	-0.0544	0.0266	0.0622	-0.0192	-0.0213	0.1715	-0.0085	0.0212	0.1673	0.0133	0.1551	152.7108	92.5023	229.6758
7	2.9182	1.265	-0.1378	2.0223	-0.3263	3.6198	0.106	0.3216	-0.0934	-0.3845	-0.0922	0.1108	0.0147	-0.2454	-0.0155	0.1949	0.0074	-0.0131	0.3007	0.0084	0.2447	141.0663	89.924	223.7835
8	0.4871	-0.0571	0.074	2.5835	0.0409	1.3406	0.008	0.0311	-0.0305	-0.3382	-0.0253	0.0655	0.1548	0.0074	0.0257	0.2281	-0.0062	-0.0054	0.2157	0.0052	0.1807	182.8616	69.4369	205.9578
9	2.4078	-0.9869	-0.4128	3.2009	0.0885	3.2723	0.0591	-0.113	0.0478	-0.0067	0.0242	-0.13	-0.0559	0.2713	-0.0495	0.1332	-0.0217	-0.0015	0.1488	0.0179	0.2252	179.9457	95.0479	223.7352
10	2.8726	-2.8103	-3.6793	2.9376	3.1111	6.2236	-0.0112	0.1474	-0.1173	0.1154	-0.003	0.186	0.4824	-0.3548	-0.0518	0.2021	-0.011	-0.0501	0.2242	0.0245	0.2526	164.9174	94.5919	216.3986
11	1.3227	0.0503	-0.0317	0.8677	-0.0708	0.9484	-0.0281	0.0418	0.0349	0.0154	0.0087	-0.0691	-0.0333	0.1268	0.0166	0.1488	-0.0091	-0.0143	0.1586	0.0057	0.1786	183.3209	87.0483	217.0952
12	1.3643	-0.1249	0.2333	1.3771	0.6644	1.0971	-0.0138	-0.007	-0.0028	-0.0187	0.0446	0.1356	0.0184	-0.0706	-0.0402	0.1287	-0.0146	0.0025	0.1496	0.0093	0.1494	177.2082	72.3696	215.0389
13	4.7955	-1.8606	2.5409	4.7435	-2.3343	5.2504	0.1103	-0.0037	-0.3517	-0.0956	0.0493	0.2545	0.1791	0.0713	-0.2742	0.1784	-0.0334	-0.001	0.1814	-0.0048	0.1791	175.9136	65.621	209.4127

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 20 through 68 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 69 through 96 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 97 through 115 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 116 through 167 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 168 through 194 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 195 through 271 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 272 through 291 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 20 through 71 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 72 through 101 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 102 through 115 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 116 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 291 )

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