PDB-9d7b: OXA-58-NA-1-157 7.5 min complex

ID or keywords:

Entry

Database: PDB / ID: 9d7b

Title

OXA-58-NA-1-157 7.5 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: 1.99 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	9d7b.cif.gz	397.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9d7b.ent.gz	328 KB	Display	PDB format
PDBx/mmJSON format	9d7b.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/d7/9d7b ftp://data.pdbj.org/pub/pdb/validation_reports/d7/9d7b	HTTPS FTP

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Related structure data

Related structure data	9d78C 9d79C 9d7aC 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
31.9 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

hetero molecules

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

Unit cell

Length a, b, c (Å)	37.012, 65.391, 192.333
Angle α, β, γ (deg.)	90.00, 91.20, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase Mass: 31455.205 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.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₇N₃O₆S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.08 Å³/Da / Density % sol: 40.78 %
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 X 16M / Detector: PIXEL / Date: Jun 5, 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: 1.99→64.1 Å / Num. obs: 61349 / % possible obs: 97.4 % / Redundancy: 5.7 % / CC_1/2: 0.991 / R_pim(I) all: 0.082 / R_rim(I) all: 0.201 / Net I/σ(I): 4.6
Reflection shell	Resolution: 1.99→2.03 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3135 / CC_1/2: 0.43

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Processing

Software

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

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.99→64.1 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2493	2967	4.89 %
R_work	0.1949	-	-
obs	0.1976	60672	96.31 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.99→64.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7863	0	4	151	8018

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8050
X-RAY DIFFRACTION	f_angle_d	1.051	10904
X-RAY DIFFRACTION	f_dihedral_angle_d	19.416	2992
X-RAY DIFFRACTION	f_chiral_restr	0.06	1177
X-RAY DIFFRACTION	f_plane_restr	0.006	1409

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 (%)
1.99-2.03	0.3638	135	0.3221	2794	X-RAY DIFFRACTION	97
2.03-2.06	0.3646	123	0.3162	2508	X-RAY DIFFRACTION	88
2.06-2.1	0.3465	102	0.3016	2139	X-RAY DIFFRACTION	80
2.1-2.14	0.3341	130	0.2674	2819	X-RAY DIFFRACTION	99
2.14-2.18	0.2817	147	0.2601	2881	X-RAY DIFFRACTION	100
2.18-2.23	0.31	145	0.2483	2766	X-RAY DIFFRACTION	100
2.23-2.28	0.3192	116	0.2709	2440	X-RAY DIFFRACTION	86
2.28-2.34	0.2843	145	0.2375	2872	X-RAY DIFFRACTION	99
2.34-2.4	0.2955	153	0.2288	2747	X-RAY DIFFRACTION	99
2.4-2.47	0.272	130	0.2145	2888	X-RAY DIFFRACTION	99
2.47-2.55	0.2801	159	0.2131	2718	X-RAY DIFFRACTION	99
2.55-2.64	0.2921	140	0.2057	2858	X-RAY DIFFRACTION	98
2.64-2.75	0.259	142	0.205	2661	X-RAY DIFFRACTION	95
2.75-2.87	0.2738	161	0.2026	2743	X-RAY DIFFRACTION	96
2.87-3.03	0.2436	145	0.2067	2813	X-RAY DIFFRACTION	99
3.03-3.22	0.3096	137	0.1963	2828	X-RAY DIFFRACTION	100
3.22-3.46	0.2202	155	0.178	2838	X-RAY DIFFRACTION	99
3.46-3.81	0.24	150	0.1697	2820	X-RAY DIFFRACTION	98
3.81-4.36	0.1954	125	0.152	2849	X-RAY DIFFRACTION	98
4.36-5.5	0.2091	164	0.1485	2794	X-RAY DIFFRACTION	97
5.5-64.1	0.1938	163	0.1614	2929	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	0.2889	0.1884	0.0404	0.1414	-0.0553	0.2478	-0.0385	-1.0621	-0.1406	0.4805	0.1892	-0.2404	-0.0179	0.4469	-0.0002	0.423	-0.0195	0.0013	0.7783	0.1238	0.4724	4.1809	-6.2056	86.008
2	1.8321	0.1934	-1.0837	0.7568	0.0818	1.6127	0.0814	-0.5931	0.1489	-0.0493	-0.0056	-0.2134	-0.3132	0.5551	0.2393	0.2363	0.002	0.0167	0.1315	0.0093	0.2395	0.1003	1.3862	69.2346
3	0.5767	0.1902	-0.1906	2.0433	-0.5209	0.9458	-0.0504	0.7307	-0.7501	0.5185	0.2485	-0.2491	-0.071	-0.236	0.0851	0.2795	0.0421	-0.0907	0.5903	-0.2207	0.5335	-14.2238	-9.0917	49.0419
4	0.1477	0.0541	-0.1517	0.4755	-0.2206	0.6504	0.4118	0.243	-1.0279	0.3661	0.0584	0.1556	0.4952	-0.5918	0.0387	0.3703	-0.0083	-0.0905	0.5608	-0.0944	0.4624	-13.8588	-11.6816	55.7171
5	1.3275	0.3625	0.5551	0.8903	-0.696	0.9946	-0.1102	0.8848	0.1158	-0.1604	0.0046	-0.0799	-0.1342	0.3131	-0.0109	0.3203	-0.0158	0.0228	0.5173	-0.038	0.2711	-3.2664	3.2365	51.9846
6	1.6373	-0.3493	0.523	1.755	-0.5396	1.5673	0.0993	0	-0.2165	0.0314	-0.0768	0.2594	-0.1613	-0.3855	-0.0002	0.2534	0.014	0.0197	0.4451	-0.0217	0.2326	-12.6975	1.3681	68.1909
7	0.694	0.5152	0.585	1.023	-0.1288	0.9422	0.0589	0.4476	-0.0971	-0.0805	-0.1328	-0.0629	0.0678	-0.3447	0.0005	0.2368	0.0038	-0.0111	0.2058	-0.0239	0.3019	-0.2176	-4.9435	65.9856
8	0.7934	0.9408	0.3936	1.9675	-0.3659	0.9132	-0.325	-0.5515	-0.4501	0.5022	0.0085	0.2217	0.1781	0.0992	-0.0016	0.3035	-0.0082	0.0181	0.4661	-0.0086	0.2793	-5.3082	-0.9773	74.8157
9	2.508	-0.3706	1.9875	1.5907	-0.0058	1.7298	0.0963	-0.4828	-0.7409	0.3094	-0.0412	-0.0496	0.6205	-0.6427	0.5862	0.3206	-0.0546	-0.0162	0.0702	0.041	0.3588	-3.6687	-10.8096	76.983
10	0.352	0.0117	-0.2437	0.0556	-0.0645	0.736	0.0143	0.4887	0.0664	0.0222	-0.0618	-0.0078	-0.9025	-0.6837	0	0.379	-0.011	0.0096	0.5522	0.0349	0.3219	-3.955	-35.0976	7.5063
11	1.1713	0.1714	0.277	0.6715	0.3142	1.4275	0.051	-0.2226	0.2646	-0.0238	-0.104	0.1737	-0.1276	-0.4224	0.0001	0.2266	-0.0025	0.025	0.3904	-0.0265	0.2893	0.1415	-26.6317	23.7578
12	1.6231	-0.2425	0.413	1.6377	-0.503	1.9195	-0.0644	-0.2843	-0.0287	0.0798	0.0757	-0.1677	0.142	0.1292	0.0002	0.2697	-0.0278	0.025	0.5606	-0.0262	0.263	12.1974	-31.5374	41.9163
13	1.8621	0.5092	0.5779	1.4217	0.9867	2.3203	0.0809	-0.1168	-0.0366	0.0671	0.0098	-0.0334	0.0007	0.1612	0.0001	0.2215	0.0003	0.0002	0.3394	0.0217	0.2602	7.1893	-27.097	28.839
14	0.7114	-0.5546	0.6005	1.5424	0.1704	0.8542	-0.0512	-0.0926	-0.126	-0.1634	-0.0861	-0.1923	0.0215	0.1864	0.0011	0.2147	-0.0353	0.0175	0.3454	0.0195	0.2885	5.2486	-29.7542	18.5773
15	0.5528	-0.1062	0.2688	0.885	0.7073	0.7656	-0.1388	0.1883	-0.5858	-0.0581	-0.1315	-0.1938	0.4387	0.4117	-0.0003	0.2644	0.0251	-0.0132	0.4088	0.0078	0.3508	3.9336	-39.3361	16.6148
16	0.2136	0.0865	0.0908	0.1443	0.061	0.2398	0.1275	-0.8164	-0.3773	-0.1946	0.169	1.0077	-0.0642	-0.245	0.0009	0.4053	0.0098	-0.0195	0.8507	0.0058	0.4588	12.206	5.6437	39.7498
17	0.8295	0.2447	-0.169	1.0272	-0.1067	1.6003	-0.0187	-0.0503	-0.1329	0.0061	-0.0243	0.1305	0.1685	-0.3635	-0	0.2155	0.0014	-0.0244	0.343	-0.0046	0.2525	16.3765	-0.5288	22.4136
18	1.747	-0.0347	-0.0543	0.7412	0.5258	0.5228	-0.0012	0.0876	0.7554	-0.2197	-0.0599	-0.011	-0.1573	0.092	-0.0063	0.3817	0.0368	-0.0262	0.729	0.083	0.4099	30.1371	11.8269	3.5866
19	2.2215	-0.5798	-0.1046	1.1828	0.3995	1.0936	-0.0771	0.144	0.0182	-0.196	0.0043	-0.003	-0.0141	-0.0069	-0.0001	0.2936	0.0007	-0.0509	0.4088	0.0102	0.2393	22.3182	1.8887	6.2328
20	1.5983	-0.3698	-0.8671	1.3887	0.4663	2.7558	0.0133	-0.0807	0.2125	-0.1585	0.0219	-0.0486	-0.029	0.4477	0.0005	0.2246	0.0156	-0.0101	0.2872	0.0001	0.2381	26.2687	1.1343	21.0813
21	0.9061	0.7231	-0.4455	1.5738	-0.1059	0.9884	-0.584	-0.2417	0.2129	0.5398	0.2188	-0.0969	-0.2327	-0.3644	-0.0198	0.2386	0.0192	-0.0234	0.4523	-0.0229	0.2415	21.5162	1.9204	27.8724
22	0.5458	0.2723	-0.2872	0.8223	0.2247	0.3283	-0.1082	-0.3786	0.4354	0.2294	-0.0063	-0.0738	-0.4799	0.3503	-0.0004	0.3499	-0.0112	-0.0138	0.4895	-0.0321	0.3211	20.1377	10.9877	31.1582
23	0.4883	-0.2243	0.7567	0.5977	-0.1055	1.2964	0.1146	0.8119	0.3638	-0.484	0.4574	-0.3477	0.8996	0.87	0.0326	0.6201	0.0516	0.0573	0.8707	0.144	0.4745	19.9085	25.554	57.9896
24	1.3176	-0.0923	0.1131	0.9347	0.34	1.6323	-0.0596	0.0997	0.077	0.0889	0.0279	-0.2548	0.2426	0.4146	-0	0.2814	0.0029	0.0156	0.4101	-0.0128	0.3163	16.593	24.3415	76.7204
25	0.4647	-0.0171	0.4092	0.1352	0.0274	0.7326	-0.1267	-0.244	0.3928	-0.2616	-0.2729	0.0445	-0.1131	-0.3765	0.0005	0.3806	0.072	0.0314	0.6244	-0.1588	0.5542	2.1986	39.393	93.8528
26	1.7175	0.5281	0.0987	0.6623	0.1763	1.8513	-0.2026	-0.2377	0.3587	0.1971	0.0149	-0.0476	-0.0688	-0.3596	0	0.3422	0.0343	0.0255	0.4215	-0.0907	0.3246	6.2462	32.1311	92.0393
27	1.6977	0.271	-0.2388	1.3689	-0.0119	1.791	0.0052	0.059	0.2313	0.1325	-0.051	0.1247	0.2348	-0.2594	0	0.2797	-0.0101	0.0384	0.3055	-0.0496	0.2842	8.6669	24.2592	83.8493
28	1.1214	-0.412	-1.0813	1.2847	-0.2904	1.4267	-0.1138	0.5519	0.766	0.0488	0.0496	0.299	-0.0692	0.013	0.0005	0.2365	0.006	0.035	0.3849	0.0451	0.3752	11.535	31.1882	76.0127
29	0.7603	-0.937	-0.442	1.4301	0.1831	0.6243	-0.0235	0.2976	0.3209	-0.5442	-0.0045	0.2753	0.008	-0.065	-0.0008	0.3083	-0.0296	-0.0204	0.4531	0.0331	0.323	11.524	25.8963	70.7299
30	1.2085	0.1883	-0.9131	0.3698	0.0469	0.8126	-0.0395	0.995	0.4862	-0.3473	0.1597	0.2044	-0.3016	-0.341	0.0218	0.3597	0.0063	0.0415	0.5084	0.1924	0.4659	13.3425	34.1872	66.4302

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 38 through 50 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 51 through 95 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 96 through 115 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 116 through 131 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 132 through 177 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 178 through 224 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 225 through 239 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 240 through 254 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 255 through 280 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 38 through 50 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 51 through 95 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 96 through 154 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 155 through 239 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 240 through 254 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 255 through 280 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 38 through 50 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 51 through 95 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 96 through 117 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 118 through 177 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 178 through 239 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 240 through 254 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 255 through 280 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 36 through 50 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 51 through 95 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 96 through 115 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 116 through 154 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 155 through 212 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 213 through 239 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 240 through 254 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 255 through 279 )

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