PDB-9d79: OXA-58-NA-1-157 1.5 min complex

ID or keywords:

Entry

Database: PDB / ID: 9d79

Title

OXA-58-NA-1-157 1.5 min complex

Components

Beta-lactamase

Keywords

HYDROLASE/INHIBITOR / beta-lactamase / carbapenemase / antibiotic resistance / inhibitor / HYDROLASE / HYDROLASE-INHIBITOR complex

Function / homology

Function and homology information

penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / plasma membrane
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.9 Å

Authors

Smith, C.A. / Maggiolo, A.O. / Toth, M. / Vakulenko, S.B.

Funding support

United States, 1items

Citation

Journal: Acs Infect Dis. / Year: 2024
Title: Decarboxylation of the Catalytic Lysine Residue by the C5 alpha-Methyl-Substituted Carbapenem NA-1-157 Leads to Potent Inhibition of the OXA-58 Carbapenemase.
Authors: Toth, M. / Stewart, N.K. / Maggiolo, A.O. / Quan, P. / Khan, M.M.K. / Buynak, J.D. / Smith, C.A. / Vakulenko, S.B.

History

Deposition	Aug 16, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2024	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9d79.cif.gz	399.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9d79.ent.gz	329 KB	Display	PDB format
PDBx/mmJSON format	9d79.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d7/9d79 ftp://data.pdbj.org/pub/pdb/validation_reports/d7/9d79	HTTPS FTP

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Related structure data

Related structure data	9d78C 9d7aC 9d7bC 9d7cC 9d7dC 9d8cC C: citing same article (ref.)
Similar structure data	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	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

C: Beta-lactamase

D: Beta-lactamase

hetero molecules

127 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

3

C: Beta-lactamase

hetero molecules

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

4

D: Beta-lactamase

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

Unit cell

Length a, b, c (Å)	37.081, 66.580, 193.165
Angle α, β, γ (deg.)	90.00, 91.13, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase Mass: 31498.209 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: blaOXA-58, bla-oxa-58, bla-oxa58, GSE42_20550, P9867_20895 Production host: Escherichia coli (E. coli) / References: UniProt: Q2TR58, beta-lactamase
#2: Chemical	ChemComp-Y33 / (5R)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid Mass: 401.478 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₇H₂₇N₃O₆S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.16 Å³/Da / Density % sol: 43.06 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium acetate, 0.1 M Tris-HCl pH 8.5, 30% PEG4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 16, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.9→39.1 Å / Num. obs: 73634 / % possible obs: 99 % / Redundancy: 7 % / CC_1/2: 0.997 / R_pim(I) all: 0.051 / R_rim(I) all: 0.138 / Net I/σ(I): 9.4
Reflection shell	Resolution: 1.9→1.94 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4520 / CC_1/2: 0.615 / R_pim(I) all: 0.551

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.1_5286: ???)	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.9→39.09 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.267	3658	4.98 %
R_work	0.2214	-	-
obs	0.2236	73506	98.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→39.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7860	0	0	198	8058

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8058
X-RAY DIFFRACTION	f_angle_d	0.978	10915
X-RAY DIFFRACTION	f_dihedral_angle_d	18.238	2992
X-RAY DIFFRACTION	f_chiral_restr	0.054	1176
X-RAY DIFFRACTION	f_plane_restr	0.008	1413

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 (%)
1.9-1.93	0.3867	147	0.3479	2598	X-RAY DIFFRACTION	97
1.93-1.95	0.3035	157	0.2907	2777	X-RAY DIFFRACTION	99
1.95-1.98	0.2829	117	0.2751	2567	X-RAY DIFFRACTION	99
1.98-2.01	0.3515	137	0.2646	2714	X-RAY DIFFRACTION	99
2.01-2.04	0.3454	143	0.262	2691	X-RAY DIFFRACTION	99
2.04-2.07	0.3163	149	0.2554	2705	X-RAY DIFFRACTION	99
2.07-2.11	0.3264	138	0.245	2594	X-RAY DIFFRACTION	98
2.11-2.15	0.2929	142	0.2455	2612	X-RAY DIFFRACTION	97
2.15-2.19	0.2697	150	0.2354	2718	X-RAY DIFFRACTION	99
2.19-2.23	0.3075	144	0.228	2658	X-RAY DIFFRACTION	99
2.23-2.28	0.2524	127	0.2292	2698	X-RAY DIFFRACTION	100
2.28-2.34	0.2652	153	0.2337	2699	X-RAY DIFFRACTION	99
2.34-2.39	0.331	150	0.2335	2684	X-RAY DIFFRACTION	100
2.39-2.46	0.3132	157	0.2376	2691	X-RAY DIFFRACTION	99
2.46-2.53	0.3352	164	0.2461	2626	X-RAY DIFFRACTION	99
2.53-2.61	0.2875	145	0.2441	2691	X-RAY DIFFRACTION	99
2.61-2.71	0.2743	124	0.2304	2720	X-RAY DIFFRACTION	99
2.71-2.81	0.3075	146	0.2261	2660	X-RAY DIFFRACTION	98
2.81-2.94	0.2672	119	0.2285	2695	X-RAY DIFFRACTION	99
2.94-3.1	0.2772	118	0.2344	2670	X-RAY DIFFRACTION	97
3.1-3.29	0.2862	138	0.227	2677	X-RAY DIFFRACTION	99
3.29-3.55	0.2487	137	0.2108	2728	X-RAY DIFFRACTION	100
3.55-3.9	0.2499	140	0.209	2726	X-RAY DIFFRACTION	100
3.9-4.47	0.2055	140	0.1867	2747	X-RAY DIFFRACTION	100
4.47-5.62	0.2294	148	0.1858	2698	X-RAY DIFFRACTION	98
5.62-39.09	0.1983	128	0.1928	2804	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	0.6385	0.5177	0.374	0.4698	0.1143	0.8793	-0.0965	-0.6689	-0.2606	0.3109	0.3172	-0.1901	0.0464	0.4604	-0.0004	0.2685	0.0162	-0.0119	0.6355	0.0828	0.3737	4.0938	-4.8427	81.4672
2	0.7597	0.1629	0.1035	0.8461	-0.5094	0.436	-0.0092	-0.2299	0.0249	0.0547	-0.1193	-0.1448	-0.1656	-0.0021	-0.0002	0.239	-0.0476	-0.0002	0.4253	-0.0013	0.2112	2.0663	1.9719	70.7375
3	1.9751	0.015	0.5181	0.8397	0.7865	1.5429	0.0108	0.4183	-0.2148	0.0224	-0.0173	-0.0847	0.0436	0.0311	0.0003	0.2578	0.0284	-0.009	0.3821	-0.0552	0.2384	-11.982	-4.2015	52.1801
4	1.5416	-0.6166	0.9514	1.5065	-0.4353	2.6437	0.031	0.0602	-0.1824	0.0252	-0.0267	0.0596	-0.2141	-0.0375	0.0001	0.2356	-0.021	0.0071	0.2405	-0.0329	0.1952	-6.9413	0.6101	64.1625
5	0.6393	0.8193	0.3771	1.1816	0.256	0.5839	-0.0415	-0.2032	-0.4252	0.3269	-0.1706	0.1774	0.1053	0.0355	-0.0021	0.2382	-0.036	0.0169	0.4615	-0.0362	0.2957	-5.1931	-1.1693	74.7296
6	0.4577	-0.0263	0.4514	0.3486	-0.3077	0.6637	0.1525	-0.3266	-0.4099	-0.0199	0.0664	0.0728	-0.1107	0.0852	-0	0.2828	-0.0494	-0.0299	0.4959	0.1251	0.3802	-3.8225	-10.7256	77.2079
7	0.1814	-0.0451	-0.0463	0.0949	0.0944	0.1624	-0.0498	0.4469	0.2069	0.1447	0.0663	0.1592	-0.2945	-0.3056	0.0012	0.3667	-0.0154	-0.0313	0.434	0.0214	0.2662	-3.7908	-35.615	7.4163
8	0.8331	0.0623	0.6456	0.6105	0.5612	0.9092	0.0179	-0.1542	0.1232	0.1135	-0.0401	0.2521	-0.1114	-0.2156	0.0006	0.1836	0.0016	0.0077	0.1618	-0.0064	0.216	0.2087	-26.9516	23.737
9	1.9727	-0.1736	0.7282	1.1762	-0.9453	1.5869	0.0156	-0.2973	-0.19	0.0721	0.0779	0.0128	0.0997	0.0949	-0.0003	0.2434	-0.0269	0.0096	0.2652	-0.0211	0.2618	12.1655	-31.8005	41.9233
10	2.1984	0.3503	0.5873	1.1913	1.0758	1.8112	0.0226	-0.1262	-0.0496	0.0808	0.0529	-0.0757	-0.0472	0.1769	0.0009	0.2036	-0.0092	-0.0001	0.1348	0	0.2002	7.2043	-27.2865	28.7605
11	0.6715	-0.4265	0.5679	0.9954	0.1176	0.7843	-0.0434	0.3887	-0.0626	0.0056	-0.0555	-0.0799	-0.2549	-0.0533	0.0005	0.222	-0.0375	0.0186	0.2484	0.0348	0.3141	5.2727	-29.9563	18.6509
12	2.2156	0.3633	0.3742	0.6786	-0.2042	0.1759	0.0942	0.5679	-0.3863	-0.2629	0.0363	0.0565	0.2946	-0.0256	0.1274	0.2449	0.0053	-0.0396	0.1489	-0.0636	0.3058	4.0599	-39.5603	16.6621
13	0.6092	0.0578	0.2821	0.6198	-0.2769	1.299	-0.0433	-0.6587	-0.0539	0.2313	0.1189	0.0918	-0.1881	-0.5025	0.0297	0.2572	-0.0032	-0.0417	0.4284	-0.0446	0.2756	12.2373	4.4066	35.411
14	0.4324	0.4223	0.3628	0.8015	0.2843	0.3055	-0.0762	0.1792	0.1533	-0.1448	-0.024	0.1567	0.1756	-0.2427	-0.0011	0.1982	0.0011	0.0012	0.2071	0.0361	0.2398	14.1621	-1.329	23.6155
15	1.8214	0.4315	0.349	0.9738	0.3785	0.3635	-0.2839	0.2411	0.38	-0.1696	0.1274	-0.1587	0.0705	0.1777	-0.0008	0.3167	-0.0091	-0.0453	0.2999	0.0395	0.2658	29.2889	9.1861	5.785
16	1.1489	0.114	-0.5362	0.5751	0.1493	0.3265	-0.166	0.7184	-0.3036	-0.2552	0.0134	0.267	0.0079	-0.2742	-0.0067	0.2748	0.0006	-0.0102	0.2421	-0.0431	0.2773	18.9707	-6.5709	5.1649
17	1.3486	0.0234	-0.2791	1.0162	0.135	2.1865	-0.0541	0.1139	0.1756	-0.0129	0.0078	-0.0046	0.0343	0.1948	0.0001	0.2036	-0.0055	-0.0134	0.1354	0.0155	0.1835	24.1959	1.1153	18.7794
18	0.703	0.2382	-0.8388	0.82	-0.0492	1.071	-0.5218	-0.0397	0.6053	0.5002	0.1559	-0.4946	-0.1042	0.1578	-0.029	0.2062	-0.0079	-0.0675	0.1618	0.0306	0.298	21.392	1.6677	27.9445
19	0.7869	0.4854	-0.4487	0.4313	-0.0442	0.9962	0.0192	-0.3514	0.4878	0.0806	-0.1787	-0.0221	-0.2409	0.1651	-0.0115	0.2898	0.0127	-0.0098	0.2284	-0.0724	0.2603	19.9509	10.7096	31.2688
20	1.5442	-0.394	0.7249	1.0407	0.9045	1.5788	-0.0184	0.0299	0.2538	0.1278	-0.0471	-0.0837	0.3364	0.3409	-0.003	0.3115	0.0265	0.0315	0.3954	0.0007	0.2973	14.6908	26.0971	75.7576
21	0.2234	-0.1771	0.0837	0.1391	-0.0663	0.0319	-1.3337	-0.5318	0.276	-0.8245	-0.0497	-0.0543	-0.473	-0.0776	-0.0529	0.8029	-0.0457	-0.0806	0.6146	-0.1067	0.6759	6.8651	47.1196	92.9145
22	2.1611	-0.2448	0.7137	0.7723	0.604	0.8704	-0.3975	-0.3534	0.5493	0.1214	0.0845	-0.3243	-0.0182	-0.4096	-0.0725	0.3718	0.0013	0.0736	0.4627	-0.1009	0.2859	6.448	31.7562	92.9008
23	1.5206	0.1048	-0.8371	1.0557	-0.5731	2.6984	-0.0575	0.1632	0.296	0.1325	-0.035	0.1905	0.1884	-0.2044	0	0.3033	-0.0377	0.0271	0.3503	-0.0482	0.3278	9.8447	26.7811	82.001
24	0.8009	-0.5376	-0.799	1.0947	0.0446	1.5693	0.0619	0.7287	0.4655	-0.3777	-0.0464	0.3539	0.1246	-0.1155	-0.0024	0.3055	-0.0297	-0.0035	0.4429	0.103	0.4092	12.5473	31.8726	68.4421

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 38 through 60 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 61 through 87 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 88 through 154 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 155 through 239 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 240 through 254 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 255 through 280 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 38 through 50 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 51 through 95 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 96 through 154 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 155 through 239 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 240 through 254 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 255 through 280 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 38 through 60 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 61 through 87 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 88 through 142 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 143 through 164 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 165 through 239 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 240 through 254 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 255 through 280 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 36 through 105 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 106 through 117 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 118 through 154 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 155 through 239 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 240 through 280 )

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About Yorodumi

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi