PDB-7afx: Crystal structure of the metallo-beta-lactamase VIM2 with 139

ID or keywords:

Entry

Database: PDB / ID: 7afx

Title

Crystal structure of the metallo-beta-lactamase VIM2 with 139

Components

Beta-lactamase VIM-2

Keywords

ANTIBIOTIC / HYDROLASE / HYDROLASES / MBL / ANTIBIOTIC RESISTANCE

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 /

molecular replacement / Resolution: 1.636 Å

Authors

Brem, J. / Schofield, C.J.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Crystal structure of the metallo-beta-lactamase VIM2 with 139
Authors: Brem, J. / Schofield, C.J.

History

Deposition	Sep 21, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 6, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model Item: _diffrn_source.pdbx_synchrotron_site

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7afx.cif.gz	270.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7afx.ent.gz	223.3 KB	Display	PDB format
PDBx/mmJSON format	7afx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7afx_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	7afx_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7afx_validation.xml.gz	22.1 KB	Display
Data in CIF	7afx_validation.cif.gz	33 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/af/7afx ftp://data.pdbj.org/pub/pdb/validation_reports/af/7afx	HTTPS FTP

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Related structure data

Related structure data	7afyC 4bz3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4c1d-1 6dd1-1 5y6d-4 1ko3-d 7cjl-1 6ew3-2 5y6e-2 4c1d-2 4nq2-d 6y6j-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	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Beta-lactamase VIM-2

B: Beta-lactamase VIM-2

hetero molecules

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

1

A: Beta-lactamase VIM-2

hetero molecules

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

2

B: Beta-lactamase VIM-2

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)	103.251, 79.066, 67.951
Angle α, β, γ (deg.)	90.000, 130.370, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Beta-lactamase VIM-2 / Class B beta-lactamase / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta- ...Class B beta-lactamase / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase VIM-2 / Metallo-beta-lactamase vim-2 / Mettalo-beta-lactamase VIM-2 / VIM-2 metallo-beta-lactamase / VIM-2 protein Mass: 25693.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255 Production host: Escherichia coli (E. coli) / Strain (production host): pLysS / References: UniProt: Q9K2N0
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-R9K / 3-(2-chlorophenyl)-7-methyl-1~{H}-indole-2-carboxylic acid Mass: 285.725 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₁₂ClNO₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.11 Å³/Da / Density % sol: 41.82 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MAGNESIUM FORMATE, 20 % W/V

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.91741 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 16, 2014

Radiation

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

Radiation wavelength

Wavelength: 0.91741 Å / Relative weight: 1

Reflection

Resolution: 1.63→29.14 Å / Num. obs: 49690 / % possible obs: 96.2 % / Redundancy: 3.4 % / B_iso Wilson estimate: 14.14 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.102 / R_pim(I) all: 0.065 / R_rim(I) all: 0.122 / Net I/σ(I): 9.3 / Num. measured all: 168749

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.63-1.67	3.3	0.712	10224	3071	0.696	0.452	0.847	1.9	80.2
7.3-29.14	3.5	0.033	1979	564	0.998	0.021	0.039	31.2	93.3

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	6.02 Å	29.14 Å
Translation	6.02 Å	29.14 Å

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Processing

Software

Name	Version	Classification
Aimless	0.3.11	data scaling
PHASER	2.5.6	phasing
PHENIX	1.12_2829	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4BZ3

4bz3

Resolution: 1.636→29.139 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1812	1993	4.01 %
R_work	0.1605	47649	-
obs	0.1614	49642	96.84 %

Solvent computation

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

Displacement parameters

B_iso max: 56.47 Å² / B_iso mean: 20.1999 Å² / B_iso min: 7.93 Å²

Refinement step

Cycle: final / Resolution: 1.636→29.139 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3451	0	96	378	3925
B_iso mean	-	-	17.94	28.97	-
Num. residues	-	-	-	-	465

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3686
X-RAY DIFFRACTION	f_angle_d	0.719	5061
X-RAY DIFFRACTION	f_chiral_restr	0.049	574
X-RAY DIFFRACTION	f_plane_restr	0.005	668
X-RAY DIFFRACTION	f_dihedral_angle_d	9.886	2141

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.6365-1.6774	0.2977	132	0.26	3146	90
1.6774-1.7228	0.2448	148	0.2317	3467	99
1.7228-1.7734	0.2498	141	0.2092	3466	99
1.7734-1.8307	0.208	144	0.1964	3435	98
1.8307-1.8961	0.2225	141	0.1865	3424	98
1.8961-1.972	0.2183	141	0.181	3436	97
1.972-2.0617	0.2056	137	0.1589	3255	94
2.0617-2.1704	0.1748	152	0.1466	3454	98
2.1704-2.3063	0.1955	140	0.145	3487	99
2.3063-2.4843	0.1604	149	0.1404	3472	99
2.4843-2.7341	0.151	146	0.1413	3463	98
2.7341-3.1294	0.1722	146	0.1443	3446	98
3.1294-3.9411	0.144	137	0.1369	3266	93
3.9411-29.1	0.1684	139	0.1647	3432	95

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	2.6573	-0.2583	0.6102	1.6126	-0.5271	1.8115	-0.0343	0.0373	0.083	-0.0676	0.0189	0.0607	-0.0153	-0.0929	-0.0086	0.1133	-0.0003	0.003	0.1004	0.0054	0.1013	-41.3409	22.6921	72.2345
2	3.5636	-0.3986	1.1792	1.8953	-0.8564	3.0085	-0.0249	-0.0156	0.2052	0.0548	-0.0061	-0.0934	-0.1532	0.0793	0.0739	0.1405	-0.0092	-0.0009	0.1003	-0.015	0.1235	-36.0364	29.016	74.8212
3	0.8073	-0.094	0.2806	2.5458	-2.3425	2.4319	0.0474	-0.1163	0.1075	0.416	0.0082	-0.0724	-0.5623	0.1032	-0.066	0.2011	-0.0075	0.0005	0.1402	-0.0185	0.1397	-36.5668	26.613	82.766
4	1.3484	0.148	0.7361	1.7131	-0.4273	1.2732	0.0003	-0.1242	-0.0817	0.0967	0.0117	0.0466	-0.0545	-0.0518	-0.0016	0.1148	-0.0058	0.0241	0.1015	0.004	0.0971	-38.7397	13.3303	80.8569
5	9.818	-0.6673	-2.9006	1.8451	0.2781	3.6646	-0.0694	-0.5553	-0.2605	0.1952	0.0592	0.0733	0.0472	-0.1002	0.0674	0.1317	-0.0043	-0.0121	0.1497	0.0254	0.107	-34.6057	9.142	89.1196
6	2.3127	-0.2564	-1.3579	1.7612	0.1285	5.5488	0.069	-0.0386	-0.0643	0.0778	0.0412	0.3176	0.2467	-0.3679	-0.0911	0.1213	-0.0153	0.0113	0.1331	0.0183	0.1586	-45.4157	7.1071	79.6762
7	6.7817	-0.7592	0.4986	1.5652	0.2229	1.4495	-0.015	-0.1312	-0.1436	0.0862	0.007	0.0523	0.0818	-0.0009	0.0182	0.1566	0.0027	-0.004	0.1166	0.0139	0.1201	-30.9453	1.5498	82.377
8	3.8576	0.5882	-1.4828	2.3514	1.3749	2.6859	-0.2151	0.1572	0.6528	0.0321	0.1251	0.7349	-0.6081	-0.6956	0.0569	0.2597	0.0837	-0.0521	0.2899	0.0158	0.3153	-33.9295	3.722	50.0792
9	2.2429	-0.52	-0.7015	2.6563	0.8293	3.1713	-0.1203	0.1324	-0.0357	-0.1407	-0.0371	0.1536	0.1233	-0.128	0.1297	0.1099	-0.0041	-0.0201	0.1073	0.0062	0.1218	-26.7435	-4.3225	47.5741
10	2.7529	0.3019	0.3114	3.4236	-1.5	8.7596	-0.0356	0.0325	0.1805	-0.2942	-0.019	0.5162	-0.0603	-0.7507	0.0616	0.1318	0.0045	-0.0597	0.1811	-0.0332	0.2125	-34.9018	-9.2152	45.6805
11	1.6455	0.4188	1.2624	1.3948	0.615	2.6843	-0.0044	0.0924	-0.0116	0.0003	-0.0008	0.0976	0.0791	-0.019	0.0183	0.1311	-0.0133	0.01	0.0971	-0	0.1276	-23.6778	-11.3909	50.8703
12	3.5085	0.5275	1.0698	1.6012	1.0049	3.6365	0.0604	-0.1849	-0.122	0.2417	-0.0266	0.0307	0.2875	-0.038	-0.0598	0.2004	0.0003	0.0115	0.0959	0.0036	0.1536	-21.3869	-17.8367	56.6955
13	0.833	0.1927	0.2582	1.7963	0.2741	0.8279	0.002	0.0334	-0.0387	-0.033	0.0149	-0.0563	0.0159	0.0873	-0.0038	0.1103	0.0014	0.0129	0.1288	-0.0033	0.1131	-14.2235	-5.4745	53.7373
14	3.6	-0.3849	-2.435	2.7617	0.9507	1.9642	0.0221	-0.1138	0.0527	-0.1115	0.0649	-0.3193	-0.1079	0.257	-0.0485	0.1027	-0.0116	0.0017	0.1377	-0.0071	0.1155	-5.4479	1.2421	56.3322
15	5.8737	-0.4596	-2.4048	1.5889	0.8173	2.7297	0.0374	0.3022	0.3336	-0.4042	-0.0153	-0.0287	-0.205	0.0236	-0.0196	0.1686	-0.0167	-0.0083	0.1137	0.0244	0.1074	-16.0944	3.6248	46.5835
16	2.2012	0.1462	0.7813	2.0003	0.3501	7.5391	-0.0729	-0.0279	0.1603	-0.0342	0.0426	-0.0015	-0.2269	0.1645	0.0347	0.1151	-0.0081	0.0026	0.1096	-0.0148	0.1575	-11.5069	9.4898	59.906
17	3.5463	0.8011	-0.4178	2.0843	-0.3931	0.9579	-0.0129	0.6844	-0.553	-0.3503	-0.035	0.0635	0.2475	-0.3216	0.0255	0.2283	-0.0119	-0.0388	0.2622	-0.0636	0.2467	-47.6035	9.2523	64.3225
18	4.3567	-1.3716	-1.5628	2.4134	0.7395	2.0422	0.1308	0.0053	0.1247	-0.1604	-0.0083	-0.0403	-0.1248	0.0684	-0.1006	0.132	0.0038	-0.0088	0.1261	-0.0033	0.1277	-42.2188	14.1618	67.8542
19	2.9673	0.2749	-0.5075	1.4168	-0.2777	2.107	0.0523	-0.0378	0.2058	0.0061	0.029	0.0852	-0.0826	-0.0185	-0.0985	0.1239	0.0002	0.0012	0.1284	-0.0007	0.1619	-46.1784	21.8579	71.4215
20	1.3783	0.9899	-1.0251	2.8562	-0.4434	3.6903	-0.1171	0.3666	0.1132	-0.5582	0.1456	0.4036	0.2825	-0.3568	-0.0276	0.1645	0.0045	-0.0497	0.1612	0.0127	0.1534	-48.2151	21.5347	61.8161

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 103 through 122 )	B	103 - 122
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 123 through 146 )	B	123 - 146
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 147 through 163 )	B	147 - 163
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 164 through 215 )	B	164 - 215
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 216 through 229 )	B	216 - 229
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 230 through 245 )	B	230 - 245
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 246 through 263 )	B	246 - 263
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 32 through 44 )	A	32 - 44
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 45 through 88 )	A	45 - 88
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 89 through 102 )	A	89 - 102
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 103 through 122 )	A	103 - 122
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 123 through 146 )	A	123 - 146
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 147 through 215 )	A	147 - 215
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 216 through 229 )	A	216 - 229
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 230 through 245 )	A	230 - 245
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 246 through 263 )	A	246 - 263
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 31 through 52 )	B	31 - 52
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 53 through 76 )	B	53 - 76
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 77 through 88 )	B	77 - 88
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 89 through 102 )	B	89 - 102

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