PDB-5acv: VIM-2-OX, Discovery of novel inhibitor scaffolds against the meta...

ID or keywords:

Entry

Database: PDB / ID: 5acv

Title

VIM-2-OX, Discovery of novel inhibitor scaffolds against the metallo- beta-lactamase VIM-2 by SPR based fragment screening

Components

BETA-LACTAMASE

Keywords

HYDROLASE

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / metal ion binding
Similarity search - Function

Biological species

PSEUDOMONAS AERUGINOSA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.963 Å

Authors

Christopeit, T. / Carlsen, T.J.O. / Helland, R. / Leiros, H.K.S.

Citation

Journal: J.Med.Chem. / Year: 2015
Title: Discovery of Novel Inhibitor Scaffolds Against the Metallo-Beta-Lactamase Vim-2 by Spr Based Fragment Screening
Authors: Christopeit, T. / Carlsen, T.J.O. / Helland, R. / Leiros, H.K.S.

History

Deposition	Aug 18, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 4, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 25, 2015	Group: Database references
Revision 2.0	Oct 23, 2019	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other Category: atom_site / pdbx_database_status / struct_conn 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1	Jan 10, 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 / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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	5acv.cif.gz	282.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5acv.ent.gz	234.7 KB	Display	PDB format
PDBx/mmJSON format	5acv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5acv_validation.pdf.gz	449.4 KB	Display	wwPDB validaton report
Full document	5acv_full_validation.pdf.gz	450.3 KB	Display
Data in XML	5acv_validation.xml.gz	25.8 KB	Display
Data in CIF	5acv_validation.cif.gz	38.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ac/5acv ftp://data.pdbj.org/pub/pdb/validation_reports/ac/5acv	HTTPS FTP

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Related structure data

Related structure data	5acuC 5acwC 5acxC 1ko3S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5o7n-d 6dd1-d 5n4s-d 4bz3-d 4pvo-d 5mm9-d 6ew3-d 6jn6-d 6tma-d 6o5t-d 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 (4) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #57 - Sep 2004 Catalase similarity (1) #105 - Sep 2008 Ribonuclease A similarity (2) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: BETA-LACTAMASE

B: BETA-LACTAMASE

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	100.709, 79.484, 66.845
Angle α, β, γ (deg.)	90.00, 129.92, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-2021- HOH

#1: Protein	BETA-LACTAMASE Mass: 28400.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: 301-5473 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K2N0, beta-lactamase
#2: Chemical	ChemComp-OH / HYDROXIDE ION Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 599 / 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: 1.81 Å³/Da / Density % sol: 31.9 % / Description: NONE
Crystal grow	pH: 7.2 Details: 22-27% PEG 3350, 0.2 M MAGNESIUM FORMATE, 5 MM BETA-MERCAPTOETHANOL, PH 7.2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.96→25.63 Å / Num. obs: 26390 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / B_iso Wilson estimate: 16.84 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 26.5
Reflection shell	Resolution: 1.96→2.01 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.2 / Mean I/σ(I) obs: 8.1 / % possible all: 88

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KO3

1ko3

Resolution: 1.963→25.632 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 19.84 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2094	1345	5.1 %
R_work	0.1617	-	-
obs	0.1641	26390	91.19 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.963→25.632 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3509	0	10	599	4118

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3739
X-RAY DIFFRACTION	f_angle_d	0.759	5139
X-RAY DIFFRACTION	f_dihedral_angle_d	13.206	1331
X-RAY DIFFRACTION	f_chiral_restr	0.03	579
X-RAY DIFFRACTION	f_plane_restr	0.003	686

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 (%)
1.9626-2.0328	0.2567	132	0.2004	2415	X-RAY DIFFRACTION	88
2.0328-2.1141	0.2613	103	0.2189	2083	X-RAY DIFFRACTION	77
2.1141-2.2103	0.2472	127	0.1853	2699	X-RAY DIFFRACTION	97
2.2103-2.3267	0.2315	117	0.1919	2239	X-RAY DIFFRACTION	83
2.3267-2.4724	0.2316	154	0.1677	2704	X-RAY DIFFRACTION	98
2.4724-2.6631	0.2126	149	0.1678	2607	X-RAY DIFFRACTION	96
2.6631-2.9308	0.2075	154	0.1655	2592	X-RAY DIFFRACTION	96
2.9308-3.3541	0.1964	164	0.1517	2691	X-RAY DIFFRACTION	98
3.3541-4.2227	0.1974	129	0.1327	2213	X-RAY DIFFRACTION	81
4.2227-25.6341	0.1676	116	0.1445	2802	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	4.7646	-0.6926	-1.3418	6.0242	1.7341	5.7209	-0.0525	-0.9341	-0.7484	1.1108	0.4069	-0.0819	0.7601	0.42	-0.3054	0.3836	0.0561	-0.0893	0.3885	0.0694	0.2581	-12.0295	2.2381	67.6266
2	2.4493	0.4146	1.6751	3.2334	-0.2645	2.7722	-0.0002	-0.5882	-0.1007	0.2539	-0.1263	-0.1082	0.3425	0.0037	0.1253	0.2078	0.0053	-0.0522	0.2543	-0.004	0.1308	-12.5415	7.905	62.3005
3	3.2845	-0.3418	0.3783	3.1876	0.1028	3.6464	0.0932	0.0242	-0.1782	0.0918	-0.1403	0.0136	0.1492	0.0047	0.0143	0.1107	-0.002	-0.0102	0.0851	-0.037	0.0928	-13.9969	9.2578	59.3147
4	2.6983	-1.5476	0.5035	3.0817	0.6247	3.0765	0.1402	-0.3442	-0.0129	0.4882	-0.0642	-0.0193	-0.003	0.2578	-0.0705	0.1897	-0.0791	-0.023	0.2377	0.0321	0.1229	-10.345	16.9293	62.9934
5	2.1609	-0.3293	0.2298	2.0409	0.4151	1.6288	0.0839	-0.0176	0.0141	-0.0793	-0.0393	-0.0161	-0.0958	0.0189	-0.0354	0.0932	-0.0268	0.0048	0.0901	0.0057	0.092	-18.2205	17.9151	49.9985
6	2.8555	0.78	0.3986	1.3808	-0.7388	2.1416	0.0244	-0.0341	-0.0886	-0.1061	-0.0531	0.0073	0.122	-0.0159	0.0333	0.1476	0.0162	-0.0082	0.0456	-0.019	0.1353	-21.0517	2.2339	47.805
7	7.2661	-0.5957	2.6145	5.7525	-0.0207	4.7998	0.1033	0.1563	-0.1462	-0.2845	-0.0793	0.1004	0.1359	-0.1861	-0.0157	0.1784	-0.0013	-0.0315	0.0781	-0.0121	0.094	-26.4645	-4.1305	47.2751
8	6.8561	-1.1341	-0.9908	1.1328	-0.6458	0.8391	0.0293	-0.2611	0.3451	0.1013	0.2733	-0.3982	-0.1863	0.2238	-0.0531	0.1351	-0.0712	-0.1259	0.5317	-0.1124	0.3245	-22.5364	-1.4489	79.4119
9	3.4276	0.6237	-1.5002	2.0319	0.2723	4.072	0.0093	-0.1947	0.2851	0.004	-0.1176	0.0115	-0.2759	0.4212	0.0974	0.0932	-0.0045	-0.0443	0.1589	-0.013	0.2088	-28.3451	-7.1052	81.9106
10	4.3423	1.0342	-2.3435	4.0122	-1.6914	5.4739	-0.2794	0.2742	0.1114	-0.2901	0.0396	-0.2546	0.1851	0.1455	0.2183	0.0904	0.0034	-0.0387	0.1393	-0.0041	0.1656	-30.233	-7.9809	76.7886
11	5.7151	0.0432	0.2937	4.4608	0.3778	3.4703	0.0177	0.0903	0.3377	0.1372	0.079	-0.2828	-0.0222	0.3735	-0.0843	0.0942	0.023	-0.0048	0.1123	-0.0017	0.1544	-26.8151	-15.9899	82.5164
12	3.4038	-1.0553	1.1601	2.2898	-0.6921	3.8487	0.0522	0.2203	-0.1272	-0.1087	-0.1001	0.058	0.2022	0.1578	0.0437	0.1003	-0.0011	0.0089	0.0987	-0.005	0.1315	-34.974	-21.0159	74.8276
13	1.837	-0.5548	0.8097	1.8437	-0.2493	2.3202	-0.0211	-0.0995	-0.1043	-0.0029	0.0082	0.1693	0.0754	-0.1749	0.0218	0.0751	-0.0079	0.0234	0.0921	-0.0029	0.1317	-44.1648	-14.6994	77.6005
14	3.4955	4.828	4.3775	8.1391	6.0107	7.0473	-0.0711	0.3904	0.0466	-0.723	0.1663	-0.1775	-0.303	0.366	-0.0837	0.2144	0.0421	-0.0097	0.1504	0.008	0.2251	-38.8117	-1.2828	66.8692
15	3.0755	-0.03	-0.6272	2.3655	0.2447	4.274	0.0237	-0.1336	0.1802	0.0815	-0.0882	0.2947	-0.076	-0.2112	0.0599	0.0993	0.0254	-0.0075	0.0541	-0.0174	0.1698	-46.1743	-2.7403	77.1703
16	3.7916	-0.1999	2.0941	3.1244	0.5633	7.9268	0.0894	0.2368	0.1909	-0.2231	-0.0955	0.2949	-0.3139	-0.1713	0.0008	0.1197	0.0323	-0.0394	0.1176	0.0138	0.1915	-44.8578	4.1226	68.6196
17	0	0	0	0	0	0	-5704.602	417250.7	-21082.2274	-668253.2	5704.602	-1240.131	0	0	0	0.2012	-0.0002	-0.0006	0.134	-0.0078	0.1811	-26.9956	10.7965	54.7818
18	0	0	0	0	0	0	3596.38	23691.463	-657622.683	1793.2295	11843.251	-328810.1013	258362.5	213973.96	-15439.6313	0.1161	-0.0312	-0.0017	0.1929	-0.0221	0.2675	-12.9135	31.2587	52.0476
19	0	-0	0	0	-0	0	0	9.921	0.0372	-9.921	-0	-5.1093	-0.0372	5.1093	0	0.1702	-0.0324	-0.0385	0.1771	0.0133	0.2584	-36.8632	-10.6173	67.007
20	0	0	-0	0	-0	0	329.9236	23377.66	-1138.4263	16839.347	267.568	-5298.9767	2095.2815	9.1941	-597.4916	0.3498	0.0008	-0.088	0.1006	0.006	0.2696	-36.8835	-30.8902	81.8403
21	0	-0	0	0	0	0	61957.857	-57459.82	4645.634	88502.254	-61957.85	91187.1665	0	0	0	0.2799	-0.0867	0.1143	0.2601	-0.0084	0.1235	-13.4531	30.6571	54.2048
22	0	0	0	0	0	0	135130.54	-245148	-2198008.5352	0	-0	0	923902.43	-65853.87	-135130.5446	0.3925	-0.0615	-0.1142	0.2797	0.1958	0.8639	-10.9641	30.6315	51.5836
23	0	0	-0	0	0	0	89142.68	47238.95	752959.2345	0	0	0	-541943	75384.252	-89142.6801	0.2211	-0.0878	0.1087	0.1067	0.0431	0.3602	-34.8311	-30.3905	81.0796
24	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.6003	-0.1022	-0.2942	0.2272	0.0356	0.4105	-36.8581	-30.0833	83.8635

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 29 THROUGH 41 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 42 THROUGH 63 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 64 THROUGH 76 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 77 THROUGH 103 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 104 THROUGH 222 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 223 THROUGH 279 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 280 THROUGH 297 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 29 THROUGH 41 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 42 THROUGH 61 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 62 THROUGH 76 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 77 THROUGH 103 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 104 THROUGH 149 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 150 THROUGH 222 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 223 THROUGH 238 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 239 THROUGH 279 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 280 THROUGH 297 )
17	X-RAY DIFFRACTION	17	CHAIN 'A' AND (RESID 1298)
18	X-RAY DIFFRACTION	18	CHAIN 'A' AND (RESID 1299)
19	X-RAY DIFFRACTION	19	CHAIN 'B' AND (RESID 1298)
20	X-RAY DIFFRACTION	20	CHAIN 'B' AND (RESID 1299)
21	X-RAY DIFFRACTION	21	CHAIN 'A' AND (RESID 1300)
22	X-RAY DIFFRACTION	22	CHAIN 'A' AND (RESID 1301)
23	X-RAY DIFFRACTION	23	CHAIN 'B' AND (RESID 1300)
24	X-RAY DIFFRACTION	24	CHAIN 'B' AND (RESID 1301)

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