PDB-5ew0: Crystal structure of the metallo-beta-lactamase Sfh-I in complex ...

ID or keywords:

Entry

Database: PDB / ID: 5ew0

Title

Crystal structure of the metallo-beta-lactamase Sfh-I in complex with the bisthiazolidine inhibitor L-CS319

Components

Beta-lactamase

Keywords

HYDROLASE / inhibitor / carbapenemase / antibiotic resistance

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / zinc ion binding
Similarity search - Function

Biological species

Serratia fonticola (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 Å

Authors

Hinchliffe, P. / Tooke, C.L. / Spencer, J.

Funding support

United States, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Cross-class metallo-beta-lactamase inhibition by bisthiazolidines reveals multiple binding modes.
Authors: Hinchliffe, P. / Gonzalez, M.M. / Mojica, M.F. / Gonzalez, J.M. / Castillo, V. / Saiz, C. / Kosmopoulou, M. / Tooke, C.L. / Llarrull, L.I. / Mahler, G. / Bonomo, R.A. / Vila, A.J. / Spencer, J.

History

Deposition	Nov 20, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 1, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jul 20, 2016	Group: Database references
Revision 1.2	Mar 30, 2022	Group: Author supporting evidence / Database references / Derived calculations Category: database_2 / pdbx_audit_support / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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
Revision 1.3	Jan 10, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ew0.cif.gz	208.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5ew0.ent.gz	165.4 KB	Display	PDB format
PDBx/mmJSON format	5ew0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5ew0_validation.pdf.gz	459.2 KB	Display	wwPDB validaton report
Full document	5ew0_full_validation.pdf.gz	463.7 KB	Display
Data in XML	5ew0_validation.xml.gz	25 KB	Display
Data in CIF	5ew0_validation.cif.gz	38.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ew/5ew0 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/5ew0	HTTPS FTP

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Related structure data

Related structure data	4nq6C 5ev6C 5ev8C 5evbC 5evdC 5evkC 5ewaC 3sd9S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3q6v-2 3sd9-1 3sd9-2 1x8i-d 3f9o-d 1x8h-d 5quh-d 2pe7-d 6nfl-d 3q6v-1 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	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	32.770, 86.700, 72.230
Angle α, β, γ (deg.)	90.00, 90.09, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 41 - 268 / Label seq-ID: 6 - 233

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	Beta-lactamase / Metallo-beta-lactamase class B2 Sfh-I Mass: 26317.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia fonticola (bacteria) / Gene: sfhI / Plasmid: pOPIN-F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): solu / References: UniProt: Q9RMI1, beta-lactamase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-3C7 / (3R,5R,7aS)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid Mass: 237.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₁NO₂S₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.95 Å³/Da / Density % sol: 36.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium acetate, 27% w/v PEG 3350, pH 7.0

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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: Jan 24, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.501
1	1	h,-k,-l	2	0.499

Reflection

Resolution: 1.3→19.42 Å / Num. obs: 91618 / % possible obs: 97.6 % / Redundancy: 5.8 % / R_merge(I) obs: 0.118 / Net I/σ(I): 7.6

Reflection shell

Resolution: 1.3→1.32 Å / Redundancy: 9.9 % / R_merge(I) obs: 0.521 / Mean I/σ(I) obs: 4.2 / % possible all: 95.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3SD9

3sd9

Resolution: 1.3→19.42 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.953 / SU B: 1.192 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18863	4742	4.9 %	RANDOM
R_work	0.16018	-	-	-
obs	0.16159	91618	96.98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 11.754 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.7 Å²	0 Å²	-0.45 Å²
2-	-	-1.95 Å²	0 Å²
3-	-	-	2.65 Å²

Refinement step

Cycle: 1 / Resolution: 1.3→19.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3622	0	28	603	4253

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	3844
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	3632
X-RAY DIFFRACTION	r_angle_refined_deg	1.569	1.97	5247
X-RAY DIFFRACTION	r_angle_other_deg	1.441	3.003	8406
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.236	5	484
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.673	25.26	173
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.481	15	661
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.929	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	585
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	4390
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	858
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.14	0.54	1888
X-RAY DIFFRACTION	r_mcbond_other	1.14	0.541	1889
X-RAY DIFFRACTION	r_mcangle_it	1.713	0.805	2373
X-RAY DIFFRACTION	r_mcangle_other	1.712	0.806	2374
X-RAY DIFFRACTION	r_scbond_it	1.97	0.725	1956
X-RAY DIFFRACTION	r_scbond_other	1.966	0.725	1956
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.883	1.015	2870
X-RAY DIFFRACTION	r_long_range_B_refined	5.624	6.512	5135
X-RAY DIFFRACTION	r_long_range_B_other	5.322	5.418	4761
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 14546 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.298→1.332 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.305	328	-
R_work	0.272	6184	-
obs	-	-	89.24 %

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	3.0713	-0.0303	-1.7354	0.0072	0.0184	0.9874	0.0111	0.0187	-0.0002	-0.0168	-0.0166	0.0171	0.0092	-0.0216	0.0055	0.0933	0.0137	-0.0333	0.0727	-0.0356	0.0452	9.555	-3.6711	68.1563
2	0.2414	-0.1009	-0.319	0.4036	-0.1303	0.6234	0.012	0.0261	-0.0369	-0.0597	-0.0369	0.0451	0.0386	0.0008	0.0249	0.0486	0.009	-0.0132	0.0585	-0.0058	0.0093	11.7712	-6.6373	75.4694
3	0.4646	0.114	-0.1658	0.5348	0.0028	0.6053	0.0165	0.0297	-0.0653	-0.0401	-0.0269	-0.036	0.0371	0.0235	0.0104	0.0464	0.0141	-0.0079	0.0454	-0.0011	0.0116	16.4821	-8.795	76.1092
4	0.5562	0.1267	-0.0191	0.3337	-0.2684	0.2935	0.0255	-0.0646	-0.0357	0.0132	-0.0149	-0.0067	0.0204	0.0037	-0.0106	0.0436	0.0009	-0.0161	0.0557	0.0095	0.0082	12.8055	-7.9609	89.8655
5	0.9736	0.5473	-0.0004	0.4301	-0.1637	0.2543	0.0819	-0.0408	-0.0435	0.1033	-0.0492	-0.0171	-0.0349	0.0402	-0.0327	0.0802	0.0028	-0.0206	0.061	0.0163	0.0229	22.5858	-5.3297	90.1694
6	0.3077	0.0158	-0.1216	0.4695	-0.108	0.4315	0.0366	-0.0081	0.0123	0.0211	-0.0302	-0.0035	-0.0623	0.0205	-0.0064	0.0496	-0.0033	-0.0045	0.0526	0.0041	0.0018	14.538	9.5518	82.6527
7	0.6325	-0.2952	-0.1596	0.7939	-0.6437	0.8354	0.096	0.0681	0.0642	0.021	-0.0432	0.0009	-0.082	0.0149	-0.0528	0.0694	0.0112	-0.002	0.0724	0.0076	0.0125	13.1186	11.1661	74.3879
8	2.7616	-0.0883	0.049	3.796	0.8486	2.0836	0.1233	0.1427	0.0176	0.0172	-0.098	0.0069	-0.0694	-0.0471	-0.0253	0.04	0.0049	-0.0098	0.0468	0.0059	0.0054	6.5813	9.2483	71.466
9	2.7822	-0.0975	-2.2493	2.1157	-0.7621	3.5473	0.0736	-0.0154	0.1492	0.133	0.0226	0.0918	-0.2194	-0.1207	-0.0962	0.0516	0.0181	-0.0029	0.0516	-0.0021	0.0181	2.423	16.1606	83.3299
10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.0322	0	0	0.0322	0	0.0322	0	0	0
11	1.3872	-0.0826	1.6164	0.0422	-0.0825	1.8886	-0.03	0.0134	0.0412	-0.0798	-0.0092	-0.0403	-0.0712	0.0112	0.0392	0.1841	0.0156	0.0803	0.0727	0.0226	0.041	10.7431	9.7623	104.4624
12	0.9784	0.3337	0.9432	0.4488	0.463	0.9916	0.0095	-0.002	0.0663	-0.1192	-0.0299	-0.0748	-0.0651	-0.0214	0.0204	0.0728	0.0107	0.0367	0.0697	0.0075	0.0338	7.7135	10.0365	109.2262
13	1.9907	0.1958	0.5092	1.1931	0.6059	0.9952	0.0011	0.0109	0.0773	-0.0633	-0.0017	0.0157	-0.1073	-0.0559	0.0006	0.0484	0.0036	0.0086	0.0541	0.0021	0.005	8.9107	14.8764	116.9061
14	0.3572	-0.0287	0.2318	0.5869	0.1901	0.542	0.0235	0.0354	0.0796	-0.0724	-0.0455	0.0044	-0.0803	-0.0508	0.022	0.058	0.0173	0.0112	0.0594	0.0103	0.0217	4.1709	15.648	112.053
15	0.4594	0.2207	-0.0215	0.3854	0.2941	0.3727	0.0242	-0.059	0.0434	0.0134	-0.0172	0.0138	-0.0222	-0.0259	-0.007	0.0481	0.0019	0.0075	0.0597	-0.0122	0.0058	7.0446	13.7271	125.886
16	1.1897	0.0488	0.1548	0.6467	0.0139	0.0633	0.0262	-0.0734	0.051	0.0887	-0.0381	0.0561	-0.0033	-0.0709	0.0119	0.0441	-0.0006	0.0178	0.0935	-0.0143	0.0106	-2.7965	11.0428	126.1117
17	0.6862	-0.2488	0.7635	0.7934	0.1186	1.1914	0.055	-0.0081	-0.0419	0.0456	-0.0467	0.0756	0.0653	-0.0902	-0.0083	0.0285	-0.0069	0.0016	0.0751	-0.0087	0.0082	-0.6462	-0.0079	118.908
18	0.2094	-0.0808	0.1233	0.3511	0.1672	0.7942	0.0456	0.0237	-0.026	0.0223	-0.0327	-0.0026	0.1038	-0.0074	-0.0129	0.0597	-0.0079	-0.0058	0.0559	-0.01	0.0052	7.4085	-6.0303	117.9045
19	1.2532	1.216	1.1974	1.6591	1.1312	1.3771	0.0652	0.0347	-0.0021	-0.0325	-0.0492	-0.0995	0.0525	-0.0325	-0.0161	0.0459	0.0099	0.0224	0.081	0.0019	0.0327	10.2317	-2.0474	109.7281
20	0.7124	-0.0533	0.1738	0.8508	-0.7015	3.0181	-0.0516	-0.0024	-0.1494	0.0493	-0.0001	-0.1024	0.1328	0.1441	0.0516	0.0647	0.0145	0.0048	0.0685	-0.0047	0.047	16.5938	-9.3134	116.5222

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	41 - 49
2	X-RAY DIFFRACTION	2	A	50 - 89
3	X-RAY DIFFRACTION	3	A	90 - 111
4	X-RAY DIFFRACTION	4	A	112 - 157
5	X-RAY DIFFRACTION	5	A	158 - 169
6	X-RAY DIFFRACTION	6	A	170 - 234
7	X-RAY DIFFRACTION	7	A	235 - 249
8	X-RAY DIFFRACTION	8	A	250 - 254
9	X-RAY DIFFRACTION	9	A	255 - 268
10	X-RAY DIFFRACTION	11	B	41 - 48
11	X-RAY DIFFRACTION	12	B	49 - 74
12	X-RAY DIFFRACTION	13	B	75 - 84
13	X-RAY DIFFRACTION	14	B	85 - 111
14	X-RAY DIFFRACTION	15	B	112 - 157
15	X-RAY DIFFRACTION	16	B	158 - 169
16	X-RAY DIFFRACTION	17	B	170 - 190
17	X-RAY DIFFRACTION	18	B	191 - 238
18	X-RAY DIFFRACTION	19	B	239 - 250
19	X-RAY DIFFRACTION	20	B	251 - 268

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