PDB-5lsc: The structure of the metallo-beta-lactamase VIM-2 in complex with...

ID or keywords:

Entry

Database: PDB / ID: 5lsc

Title

The structure of the metallo-beta-lactamase VIM-2 in complex with a triazolylthioacetamide inhibitor

Components

Metallo-beta-lactamase VIM-2-like protein

Keywords

HYDROLASE / Antibiotic resistance / Carbapenemases / Verona integron-encoded metallo-beta-lactamase 2 / VIM-2

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.497 Å

Authors

Christopeit, T. / Yang, K.-W. / Yang, S.-K. / Leiros, H.-K.S.

Funding support

Norway,

China, 3items

Organization	Grant number	Country
Tromso Reserach Foundation		Norway
Research Council of Norway	218539, SYNKNOYT 2011 and 213808, FRIMEDBIO 2011	Norway
National Natural Science Foundation of China	21272186, 21572179 and 81361138018	China

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: The structure of the metallo-beta-lactamase VIM-2 in complex with a triazolylthioacetamide inhibitor.
Authors: Christopeit, T. / Yang, K.W. / Yang, S.K. / Leiros, H.K.

History

Deposition	Aug 25, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 30, 2017	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5lsc.cif.gz	304.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5lsc.ent.gz	251.7 KB	Display	PDB format
PDBx/mmJSON format	5lsc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5lsc_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5lsc_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5lsc_validation.xml.gz	27.7 KB	Display
Data in CIF	5lsc_validation.cif.gz	42 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ls/5lsc ftp://data.pdbj.org/pub/pdb/validation_reports/ls/5lsc	HTTPS FTP

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Related structure data

Related structure data	1ko3S S: Starting model for refinement
Similar structure data	4pvo-2 5ypk-7 5o7n-2 6o5t-2 5acw-1 6xbe-4 4fsb-2 5mxr-d 5k48-2 6tgi-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	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Metallo-beta-lactamase VIM-2-like protein

B: Metallo-beta-lactamase VIM-2-like protein

hetero molecules

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

1

A: Metallo-beta-lactamase VIM-2-like protein

hetero molecules

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

2

B: Metallo-beta-lactamase VIM-2-like protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	100.624, 79.255, 67.200
Angle α, β, γ (deg.)	90.00, 130.50, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-576- HOH
2	1	B-550- HOH

#1: Protein	Metallo-beta-lactamase VIM-2-like protein Mass: 25539.322 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8QIQ9
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-752 / 2-[5-[2-(1,3-benzothiazol-2-ylamino)-2-oxidanylidene-ethyl]sulfanyl-4~{H}-1,2,4-triazol-3-yl]benzoic acid Mass: 411.458 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₁₃N₅O₃S₂
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 644 / 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: 1.99 Å³/Da / Density % sol: 38.33 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 22-27% PEG 3350, 0.2 M magnesium formate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918 Å / Relative weight: 1
Reflection	Resolution: 1.497→38.255 Å / Num. obs: 63893 / % possible obs: 99.1 % / Redundancy: 3.7 % / B_iso Wilson estimate: 12.12 Å² / R_merge(I) obs: 0.048 / Net I/σ(I): 18.8
Reflection shell	Resolution: 1.497→1.52 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.309 / Mean I/σ(I) obs: 4.3 / % possible all: 93.3

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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: 1KO3

1ko3

Resolution: 1.497→38.255 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.94

	R_factor	Num. reflection	% reflection
R_free	0.1655	3161	4.95 %
R_work	0.1355	-	-
obs	0.137	63893	99.12 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.497→38.255 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3532	0	68	644	4244

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4084
X-RAY DIFFRACTION	f_angle_d	1.233	5641
X-RAY DIFFRACTION	f_dihedral_angle_d	13.507	1456
X-RAY DIFFRACTION	f_chiral_restr	0.071	624
X-RAY DIFFRACTION	f_plane_restr	0.006	768

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 (%)
1.4974-1.5198	0.2019	117	0.1899	2459	X-RAY DIFFRACTION	92
1.5198-1.5435	0.2281	130	0.1845	2656	X-RAY DIFFRACTION	100
1.5435-1.5688	0.2242	134	0.1811	2628	X-RAY DIFFRACTION	100
1.5688-1.5959	0.2383	134	0.1719	2683	X-RAY DIFFRACTION	100
1.5959-1.6249	0.1849	133	0.1645	2668	X-RAY DIFFRACTION	100
1.6249-1.6561	0.1929	145	0.158	2600	X-RAY DIFFRACTION	99
1.6561-1.6899	0.1783	120	0.156	2656	X-RAY DIFFRACTION	100
1.6899-1.7267	0.1468	159	0.1444	2641	X-RAY DIFFRACTION	100
1.7267-1.7669	0.176	143	0.1451	2642	X-RAY DIFFRACTION	100
1.7669-1.811	0.1732	143	0.1417	2668	X-RAY DIFFRACTION	100
1.811-1.86	0.1706	153	0.1452	2637	X-RAY DIFFRACTION	100
1.86-1.9147	0.1845	147	0.1416	2637	X-RAY DIFFRACTION	100
1.9147-1.9765	0.1691	130	0.138	2659	X-RAY DIFFRACTION	99
1.9765-2.0472	0.1472	132	0.1288	2639	X-RAY DIFFRACTION	100
2.0472-2.1291	0.159	126	0.1274	2669	X-RAY DIFFRACTION	100
2.1291-2.226	0.1681	151	0.1261	2653	X-RAY DIFFRACTION	100
2.226-2.3434	0.1782	142	0.1285	2626	X-RAY DIFFRACTION	100
2.3434-2.4902	0.1315	112	0.1273	2680	X-RAY DIFFRACTION	99
2.4902-2.6824	0.1672	146	0.1315	2624	X-RAY DIFFRACTION	99
2.6824-2.9522	0.1757	128	0.1331	2672	X-RAY DIFFRACTION	99
2.9522-3.3792	0.1651	169	0.1273	2613	X-RAY DIFFRACTION	99
3.3792-4.2566	0.1422	144	0.1139	2631	X-RAY DIFFRACTION	98
4.2566-38.2672	0.1463	123	0.1333	2691	X-RAY DIFFRACTION	98

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	2.1771	-0.5105	-0.3342	2.3793	0.5198	2.943	-0.0433	0.1898	0.1176	-0.0549	-0.0402	0.1081	-0.0298	-0.3395	0.0671	0.059	-0.0087	-0.0188	0.1051	0.0038	0.0967	-35.712	-7.4888	-4.3817
2	4.1427	0.1298	0.9351	3.5884	-0.1724	2.6312	-0.0321	0.1634	0.3611	-0.1171	-0.024	0.3288	-0.2813	-0.594	0.0809	0.0849	-0.003	-0.0311	0.1883	-0.0055	0.1595	-41.9575	-14.463	-6.1781
3	1.2749	0.2628	0.2605	1.7103	0.0622	1.2902	-0.0083	0.0266	-0.0402	-0.0355	-0.0105	-0.1486	0.0208	0.0594	0.0182	0.0568	-0.0017	0.007	0.0687	0.0027	0.077	-23.0372	-11.5182	1.3118
4	2.7136	0.3826	2.3449	2.1382	1.1128	3.1947	-0.0072	-0.1634	0.1537	0.114	0.0285	-0.1926	-0.3871	0.2227	-0.0228	0.1135	-0.0245	-0.0233	0.0918	-0.0077	0.1683	-19.4013	4.6162	8.3974
5	4.9009	-1.661	-0.3555	2.2072	1.7772	3.9	0.1227	0.6877	-0.6532	-0.433	0.1198	-0.0683	0.2655	-0.1351	-0.19	0.1926	-0.0264	-0.042	0.2637	-0.0808	0.1946	-51.8695	1.9958	9.3455
6	3.2799	-1.2741	-0.7006	3.374	1.3224	2.8548	0.0846	0.2291	0.0466	-0.113	-0.1331	0.0919	-0.0349	-0.1581	0.0366	0.1006	0.0113	-0.0214	0.0759	0.0003	0.0609	-52.2606	11.1999	16.3471
7	6.5059	1.1585	-0.6887	2.6999	-0.5798	2.7016	0.0304	0.6025	-0.1378	-0.6182	-0.1091	0.2304	-0.0368	-0.1997	0.056	0.3776	0.1031	-0.0626	0.2064	-0.0295	0.1203	-55.5443	16.3676	9.4328
8	3.3268	-0.7441	0.976	2.1243	-0.0931	2.0719	-0.0027	0.0568	0.1384	-0.1265	-0.0463	-0.0419	-0.2182	0.0104	0.057	0.1296	-0.0012	0.0097	0.0511	-0.0025	0.0687	-45.4131	21.8745	21.607
9	2.0516	-0.4686	0.3618	2.0606	-0.0101	0.8788	-0.0451	-0.1633	0.0533	0.2068	0.021	-0.0215	-0.165	-0.074	0.0139	0.1165	0.0123	-0.0044	0.0848	-0.0159	0.0567	-45.2304	17.9146	31.3824
10	1.4696	0.5377	0.8222	2.9454	0.2395	1.696	0.0276	0.0201	-0.1176	-0.0389	0.0622	-0.0996	0.0992	0.039	-0.0848	0.0902	-0.005	-0.0085	0.0487	0.0142	0.0602	-44.5077	4.7087	25.6721
11	2.489	0.3564	-0.1848	1.8413	0.003	2.4401	0.0667	-0.2435	-0.1511	0.1991	-0.0096	0.0903	0.1431	-0.2104	-0.0457	0.0971	-0.0016	0.0078	0.0654	0.0237	0.0806	-47.9674	3.1119	31.7706
12	7.1597	0.6449	-0.5894	2.3615	-0.3782	3.3054	-0.1009	-0.1931	-0.4729	0.2004	0.0383	-0.3302	0.2748	0.2637	0.0692	0.1446	0.0229	-0.0416	0.0736	0.0105	0.1317	-38.078	-3.7663	29.8571
13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.1118	-0.011	-0.0003	0.1077	-0.0071	0.1306	-27.6759	-9.7272	9.228
14	0	0	0	0	0	0	0	0	-0	-0	0	-0	-0	0	-0	0.1271	-0.0031	-0.005	0.13	-0.006	0.1376	-29.4921	-7.163	6.948
15	0	-0	-0	0	0	0	-9921.0482	-64408.3393	4495.475	131747.4538	27902.948	-535515.7159	39684.1927	257633.3573	-17981.8998	0.1858	0.031	-0.0104	0.105	-0.015	0.2169	-27.5069	-30.3446	-4.6487
16	0	0	0	0	0	0	0	-0	-1004.7161	0	-0	-4018.8643	1004.7161	4018.8643	-0	0.1464	-0.004	0.0241	0.1078	-0.0039	0.1385	-38.3294	11.1538	21.8538
17	-0	0	0	0	0	0	0	-0	-0	-0	0	-13912.3566	0	13912.3566	-0	0.1385	-0.0048	0.0051	0.1307	-0.0124	0.1349	-40.8054	8.683	20.0982
18	0	0	0	0	0	0	-11533.2185	219302.2591	381776.398	-361049.2348	-26662.817	38196.0355	-369747.1273	-26662.817	38196.0355	0.1422	0.0201	-0.0302	0.0927	-0.008	0.1566	-51.8771	31.6831	24.6351
19	0	0	-0	0	-0	0	22378.7825	34136.8009	49717.9239	40256.2496	-737.2162	1038534.164	-56866.7211	-340725.0642	-21641.5663	0.2669	0.0447	0.1036	0.1315	0.013	0.4221	-29.4821	-29.8175	-3.8531
20	0	0	-0	0	0	0	0	0	-0	0	0	0	-0	-0	-0	0.5579	0.042	-0.0276	0.1473	-0.0066	0.2089	-27.3169	-29.9843	-6.8007
21	0	0	-0	0	0	0	-25881.2856	23022.2465	-401322.0808	0	-0	0	964931.8158	38652.7663	25881.2856	0.3823	0.0351	0.0228	0.0778	-0.0185	0.1607	-51.3435	31.0972	22.5463
22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.3164	0.0637	-0.1596	0.2073	-0.0452	0.5062	-53.9278	31.4295	24.8664
23	9.2968	0.595	3.5885	9.2115	-2.3753	5.3949	0.1661	-0.4196	0.1393	0.1066	0.1358	0.5487	0.2769	-0.7088	-0.2839	0.1512	-0.0074	0.04	0.1771	-0.0094	0.1299	-32.9912	-8.6336	9.9289
24	8.3241	4.9983	-3.0121	8.7773	-5.1026	2.9716	0.0439	0.5264	0.3501	-0.598	0.0632	0.0413	-0.3776	0.2623	-0.101	0.2171	-0.0106	0.0379	0.2174	-0.0197	0.1511	-38.1854	10.2693	16.412
25	0	0	0	0	0	0	0	0	0	0	0	-5678.8476	-0	5678.8476	-0	0.2391	-0.0309	0.0666	0.2549	-0.0178	0.1617	-31.1068	-14.005	12.5782
26	0	0	-0	0	0	0	-48303.1033	-5456.5765	-313210.8844	0	-0	0	294732.9322	-2232.2358	48303.1033	0.2494	-0.0024	0.0773	0.2696	0.0104	0.2591	-35.3543	15.6826	18.2865

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 88 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 89 through 103 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 104 through 279 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 280 through 298 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 28 through 41 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 42 through 88 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 89 through 103 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 104 through 149 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 150 through 200 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 201 through 238 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 239 through 279 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 280 through 298 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 1 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 2 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 3 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 1 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 2 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 3 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 401 )
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 402 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 401 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 402 )
23	X-RAY DIFFRACTION	23	chain 'A' and (resid 404 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 404 )
25	X-RAY DIFFRACTION	25	chain 'A' and (resid 403 )
26	X-RAY DIFFRACTION	26	chain 'B' and (resid 403 )

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi