PDB-9d8c: OXA-58-NA-1-157 2.5 hour complex

ID or keywords:

Entry

Database: PDB / ID: 9d8c

Title

OXA-58-NA-1-157 2.5 hour 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: 2.15 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 19, 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	9d8c.cif.gz	396.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9d8c.ent.gz	327.6 KB	Display	PDB format
PDBx/mmJSON format	9d8c.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/d8/9d8c ftp://data.pdbj.org/pub/pdb/validation_reports/d8/9d8c	HTTPS FTP

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Related structure data

Related structure data	9d78C 9d79C 9d7aC 9d7bC 9d7cC 9d7dC 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)	37.147, 66.106, 193.165
Angle α, β, γ (deg.)	90.00, 91.19, 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.11 Å³/Da / Density % sol: 41.83 %
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 10, 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: 2.15→39 Å / Num. obs: 50713 / % possible obs: 99.1 % / Redundancy: 7.1 % / CC_1/2: 0.995 / R_pim(I) all: 0.072 / R_rim(I) all: 0.194 / Net I/σ(I): 6.7
Reflection shell	Resolution: 2.15→2.22 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4397 / CC_1/2: 0.619 / R_pim(I) all: 0.566

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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: 2.15→38.99 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2773	2515	4.97 %
R_work	0.2166	-	-
obs	0.2197	50643	98.92 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.15→38.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7868	0	0	80	7948

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8059
X-RAY DIFFRACTION	f_angle_d	1.045	10920
X-RAY DIFFRACTION	f_dihedral_angle_d	17.971	2998
X-RAY DIFFRACTION	f_chiral_restr	0.057	1180
X-RAY DIFFRACTION	f_plane_restr	0.007	1411

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 (%)
2.15-2.19	0.3607	130	0.3023	2693	X-RAY DIFFRACTION	98
2.19-2.24	0.3315	156	0.2828	2580	X-RAY DIFFRACTION	99
2.24-2.28	0.3575	151	0.2738	2663	X-RAY DIFFRACTION	100
2.28-2.34	0.3159	140	0.2605	2674	X-RAY DIFFRACTION	99
2.34-2.4	0.3146	153	0.2528	2631	X-RAY DIFFRACTION	100
2.4-2.46	0.3247	123	0.2568	2746	X-RAY DIFFRACTION	100
2.46-2.53	0.3572	118	0.2473	2680	X-RAY DIFFRACTION	100
2.53-2.62	0.3313	113	0.251	2708	X-RAY DIFFRACTION	100
2.62-2.71	0.2861	149	0.2333	2665	X-RAY DIFFRACTION	99
2.71-2.82	0.2915	159	0.2252	2646	X-RAY DIFFRACTION	98
2.82-2.95	0.3056	134	0.2294	2631	X-RAY DIFFRACTION	98
2.95-3.1	0.3082	136	0.2417	2616	X-RAY DIFFRACTION	96
3.1-3.29	0.3241	135	0.2377	2678	X-RAY DIFFRACTION	99
3.29-3.55	0.299	155	0.21	2651	X-RAY DIFFRACTION	100
3.55-3.91	0.2871	139	0.1977	2691	X-RAY DIFFRACTION	99
3.91-4.47	0.2337	152	0.1818	2731	X-RAY DIFFRACTION	100
4.47-5.63	0.2157	135	0.1805	2686	X-RAY DIFFRACTION	99
5.63-38.99	0.2049	137	0.1873	2758	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	0.3094	0.2496	-0.0029	0.2208	-0.0052	0.2413	-0.2597	-0.68	-0.6876	0.1222	0.4304	-0.0931	-0.4699	0.8728	0.0008	0.4163	-0.0955	-0.0542	0.8723	0.1524	0.4762	4.0275	-5.9545	86.3579
2	1.8686	0.5622	0.8002	0.3232	0.6746	1.7355	-0.0138	-0.2149	-0.0225	-0.186	0.069	-0.1232	-0.3313	0.2121	-0.0013	0.3146	-0.0394	0.0138	0.485	0.0166	0.3132	0.0161	1.4232	69.4635
3	0.9804	-0.2079	-0.6122	1.1468	0.1709	0.3925	0.2189	0.9105	-0.4894	0.567	-0.348	-0.2704	-0.0174	-0.2791	0.0034	0.3959	0.1003	-0.1068	0.4902	-0.1789	0.5996	-14.0209	-9.9582	50.0647
4	2.5998	-0.3275	0.8622	1.0244	-0.7884	2.0095	-0.0443	0.5457	-0.0993	0.0033	0.0774	-0.1191	0.018	0.1363	0.0001	0.3928	-0.0192	0.0248	0.4912	-0.0662	0.2882	-6.0269	-0.2881	53.2411
5	1.836	-1.0565	0.4815	1.2035	-0.9503	2.985	0.2005	-0.1286	-0.3402	-0.0516	-0.1075	0.1634	-0.3279	-0.3006	0.0004	0.3273	-0.0011	0.0021	0.3167	-0.0205	0.3178	-10.0025	-0.1241	68.0163
6	0.9044	0.8577	0.9248	1.5705	0.3789	1.2439	0.3668	-0.6956	0.0237	-0.2308	-0.3043	-0.0866	-0.2593	0.2659	0.0051	0.3545	-0.127	-0.0355	0.5585	-0.0415	0.3468	-5.1155	-1.2016	74.8105
7	0.7551	0.3462	0.1278	0.5518	-0.1611	0.6109	0.21	0.0294	-0.6869	0.1167	-0.3204	-0.137	0.1079	-0.2658	-0.0075	0.3888	-0.0687	-0.0466	0.5578	0.1686	0.4936	-3.8148	-10.7355	77.3936
8	1.6645	0.285	0.5105	0.7285	-0.3818	1.2929	0.0188	0.0982	0.1931	-0.0561	-0.0202	0.2251	-0.0799	-0.291	-0.0001	0.326	0.0172	0.0183	0.3274	0.0018	0.3573	-0.8257	-28.8383	19.9523
9	0.9239	-0.6563	0.6895	1.0528	-1.0339	0.9801	0.0392	-0.3812	-0.328	0.1593	-0.0077	-0.0711	0.2895	0.1181	0.0011	0.4221	0.0133	0.0329	0.4694	-0.0031	0.4926	14.7467	-37.0864	41.8349
10	2.2982	-0.435	0.6426	0.7428	0.8204	1.5167	-0.1352	-0.2847	0.1048	0.0217	0.0965	0.1453	0.0174	-0.0134	0.0001	0.3396	-0.0093	0.0237	0.2012	-0.0339	0.3372	5.3624	-22.7991	36.2144
11	0.8095	0.5324	0.7629	1.48	1.6212	1.8182	-0.0264	0.3307	-0.2167	0.0206	0.247	-0.2414	0.0616	0.4259	-0	0.3155	0.022	-0.0246	0.3584	0.0017	0.3921	10.5193	-31.8872	25.3298
12	0.6609	-0.1832	0.7768	0.9518	0.1578	1.0569	0.3739	0.0299	0.4633	0.054	-0.0849	0.3221	-0.2141	0.4759	0.0002	0.3185	-0.0707	0.0355	0.4598	-0.0206	0.3935	5.2527	-29.9149	18.695
13	0.4914	-0.0366	0.5133	1.1276	0.2846	0.6257	0.1073	0.3197	-0.3399	-0.003	-0.0057	-0.0531	0.2113	0.4146	-0.0001	0.2913	0.0173	-0.0441	0.4302	-0.0503	0.4804	3.9922	-39.5195	16.6625
14	0.9868	0.6312	-0.719	0.5764	-0.5822	1.1164	-0.0869	-0.7493	0.1117	0.4909	0.0716	0.1738	-0.4197	0.1963	0.0006	0.4154	-0.0207	-0.027	0.5236	-0.0374	0.4467	12.2102	4.4574	35.3868
15	0.8468	0.8955	0.1489	0.9172	0.2919	0.8798	-0.1475	0.3021	-0.094	-0.2159	-0.0472	0.1561	0.3015	-0.4314	-0.0192	0.2548	-0.0164	-0.0037	0.2627	0.0316	0.2711	17.3236	-1.6717	20.6928
16	1.0342	0.8071	0.6424	0.8605	0.6318	0.4614	-0.0892	0.514	0.4563	-0.3327	-0.1754	0.1111	0.0571	0.1034	-0.0001	0.4723	-0.0368	-0.0944	0.5346	0.0452	0.4649	30.0902	11.9194	3.8103
17	2.3818	-1.3932	0.1441	1.485	-0.8158	0.8241	-0.1227	0.2178	0.2136	-0.2436	0.0012	0.1259	-0.0314	0.1112	-0.0002	0.3906	-0.0164	-0.0303	0.4068	0.0152	0.2789	24.3372	2.0988	5.9809
18	1.3073	0.007	-0.736	1.0308	0.1759	3.4692	-0.0545	0.0526	0.1311	-0.0385	0.0378	0.0535	0.0735	0.1898	-0.0001	0.2757	0.0119	-0.0181	0.2127	0.0047	0.2888	24.2929	1.1805	18.7945
19	1.1791	0.8024	-1.2539	1.4238	-0.3468	1.6028	-0.375	-0.3665	0.1339	0.9214	0.2361	-0.13	0.0546	0.2806	0.0087	0.3215	0.0104	-0.0703	0.2964	-0.0141	0.3461	21.4288	1.7587	27.9795
20	0.6367	0.5315	-1.2385	0.4677	-1.1537	2.9901	0.2203	-0.3067	0.4263	0.3081	-0.3589	0.0328	-0.3626	0.6429	-0.0834	0.4292	0.0235	-0.0195	0.2978	-0.1333	0.3611	20.0242	10.7814	31.2595
21	0.5209	-0.5129	-0.3505	2.0643	1.2348	0.8609	0.3204	0.3892	0.0881	-0.0343	0.4741	-0.386	0.6225	0.5069	0.1017	0.7063	0.219	0.0691	0.7497	0.2376	0.516	19.9762	26.0555	58.3325
22	1.0704	-0.6605	-0.2511	0.6615	0.7357	1.6691	-0.2426	-0.0965	0.2733	0.294	0.0732	-0.19	0.3137	0.8357	-0.0497	0.4203	-0.005	0.0374	0.4647	-0.0443	0.3534	16.7175	24.7284	77.1263
23	4.3859	2.1983	1.0229	1.5095	1.226	1.475	-0.4539	-0.4668	0.7612	-0.5597	-0.6629	0.4257	-0.0852	-0.599	-0.4867	0.4154	0.0667	0.0305	0.7535	-0.0795	0.4333	2.6672	40.2681	93.7613
24	1.0932	0.0258	-0.0341	0.7915	0.4353	0.2345	-0.2231	-0.2208	0.8357	0.2655	0.0936	0.0318	-0.3579	-0.259	-0.0144	0.5284	0.0449	0.0321	0.6308	-0.1217	0.5116	4.2169	37.2798	91.2853
25	0.8046	-0.5253	0.0143	0.353	0.08	0.5587	-0.1135	-0.4539	0.0709	0.1769	0.1333	-0.0311	0.337	0.661	-0.0006	0.4159	0.0001	-0.0002	0.4712	-0.0545	0.3119	15.5263	24.5506	93.7049
26	1.1576	-0.1197	0.1142	1.1234	0.0043	2.5437	-0.0185	0.2884	0.4573	0.0787	-0.0335	0.2555	0.2488	-0.3133	0.0005	0.3832	-0.0714	0.0256	0.4886	-0.0278	0.4414	6.7346	26.6798	78.1137
27	0.9306	-0.6957	-0.9754	1.0433	0.6487	1.0118	-0.3108	0.8459	0.2517	-0.3292	0.3646	-0.0049	0.1548	0.3966	-0.0013	0.4681	-0.0609	0.0127	0.4323	0.06	0.5129	11.6603	26.211	71.2642
28	0.6137	-0.124	-0.6743	0.3643	0.335	0.8683	-0.2857	1.0888	0.8115	-0.6117	-0.0034	0.6246	-0.2431	-0.2225	-0.0789	0.4213	-0.0385	-0.04	0.5863	0.1969	0.6024	12.9736	34.7045	66.4884

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 117 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 118 through 177 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 178 through 239 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 240 through 254 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 255 through 280 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 38 through 95 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 96 through 131 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 132 through 196 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 197 through 239 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 240 through 254 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 255 through 280 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 38 through 60 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 61 through 95 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 96 through 117 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 118 through 164 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 165 through 239 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 240 through 254 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 255 through 280 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 36 through 50 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 51 through 95 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 96 through 117 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 118 through 142 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 143 through 177 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 178 through 239 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 240 through 254 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 255 through 280 )

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

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Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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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