PDB-9d7a: OXA-58-NA-1-157 5 min complex

ID or keywords:

Entry

Database: PDB / ID: 9d7a

Title

OXA-58-NA-1-157 5 min complex

Components

(Beta-lactamase) x 2

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: 2.05 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	9d7a.cif.gz	398.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9d7a.ent.gz	327.9 KB	Display	PDB format
PDBx/mmJSON format	9d7a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9d7a_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9d7a_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9d7a_validation.xml.gz	41.6 KB	Display
Data in CIF	9d7a_validation.cif.gz	52.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d7/9d7a ftp://data.pdbj.org/pub/pdb/validation_reports/d7/9d7a	HTTPS FTP

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Related structure data

Related structure data	9d78C 9d79C 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

128 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)	37.065, 66.257, 193.061
Angle α, β, γ (deg.)	90.00, 91.12, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase Mass: 31498.209 Da / Num. of mol.: 3 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: Protein	Beta-lactamase Mass: 31455.205 Da / Num. of mol.: 1 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
#3: 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
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.15 Å³/Da / Density % sol: 42.75 %
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 18, 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: 2.05→39.01 Å / Num. obs: 58348 / % possible obs: 99.1 % / Redundancy: 7.1 % / CC_1/2: 0.996 / R_pim(I) all: 0.063 / R_rim(I) all: 0.168 / Net I/σ(I): 7.3
Reflection shell	Resolution: 2.05→2.11 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4506 / CC_1/2: 0.665 / R_pim(I) all: 0.523

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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: 2.05→39.01 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2926	2809	4.82 %
R_work	0.2397	-	-
obs	0.2423	58264	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: 2.05→39.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7882	0	0	85	7967

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8087
X-RAY DIFFRACTION	f_angle_d	1.089	10956
X-RAY DIFFRACTION	f_dihedral_angle_d	18.917	3011
X-RAY DIFFRACTION	f_chiral_restr	0.055	1181
X-RAY DIFFRACTION	f_plane_restr	0.007	1417

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 (%)
2.05-2.09	0.377	135	0.3368	2760	X-RAY DIFFRACTION	99
2.09-2.12	0.3589	150	0.2926	2737	X-RAY DIFFRACTION	99
2.12-2.16	0.3464	165	0.2726	2799	X-RAY DIFFRACTION	100
2.16-2.21	0.301	126	0.2666	2734	X-RAY DIFFRACTION	99
2.21-2.26	0.3146	130	0.2661	2749	X-RAY DIFFRACTION	100
2.26-2.31	0.3376	146	0.2702	2796	X-RAY DIFFRACTION	99
2.31-2.37	0.3037	126	0.2601	2747	X-RAY DIFFRACTION	99
2.37-2.43	0.3238	123	0.2634	2765	X-RAY DIFFRACTION	99
2.43-2.5	0.3195	132	0.2607	2727	X-RAY DIFFRACTION	98
2.5-2.58	0.4207	123	0.261	2749	X-RAY DIFFRACTION	98
2.58-2.67	0.3433	161	0.2564	2776	X-RAY DIFFRACTION	100
2.67-2.78	0.2993	132	0.2506	2785	X-RAY DIFFRACTION	100
2.78-2.91	0.314	138	0.2492	2827	X-RAY DIFFRACTION	100
2.91-3.06	0.2894	149	0.2622	2783	X-RAY DIFFRACTION	100
3.06-3.25	0.3119	133	0.264	2732	X-RAY DIFFRACTION	98
3.25-3.5	0.2927	158	0.2394	2751	X-RAY DIFFRACTION	98
3.5-3.86	0.2704	146	0.2257	2748	X-RAY DIFFRACTION	97
3.86-4.41	0.26	131	0.2092	2820	X-RAY DIFFRACTION	99
4.41-5.56	0.2589	157	0.2088	2809	X-RAY DIFFRACTION	99
5.56-39.01	0.2441	148	0.2095	2861	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	0.5376	0.5252	0.2715	0.5344	0.0211	0.7979	0.1037	-0.4779	-0.565	0.1248	0.0192	-0.0564	-0.0127	0.5867	-0.0005	0.2999	-0.04	-0.0114	0.6615	0.0646	0.4355	3.999	-4.782	81.798
2	1.7776	0.0275	0.2865	-0.2529	0.1375	-0.1024	-0.0336	0.0278	0.2076	-0.095	-0.0669	-0.0812	-0.2752	0.17	-0.0003	0.3646	0.0141	-0.0088	0.4052	0.0279	0.3256	-5.233	1.665	63.731
3	0.1391	-0.0865	-0.2432	0.4851	0.3446	0.5218	0.2294	0.7424	-1.325	-0.0343	-0.009	-0.173	-0.1964	-0.4638	0.0334	0.3605	-0.0221	-0.0292	0.6006	-0.2072	0.6578	-12.151	-13.998	53.029
4	2.4359	-0.5456	0.6093	0.9215	-0.8444	2.5154	0.0811	0.4112	-0.1392	-0.0044	-0.0949	0.0016	-0.2133	-0.0272	-0.0002	0.3231	0.0003	0.0096	0.3136	-0.0336	0.29	-7.11	1.225	61.409
5	1.0868	1.0067	-0.1229	1.2693	-0.1483	0.8609	0.0372	-0.2694	-1.0516	0.2673	-0.576	0.3239	0.2386	0.2038	-0.0468	0.3698	-0.0479	-0.0099	0.4602	-0.0503	0.4094	-2.235	-5.959	72.534
6	0.1778	-0.1646	0.1434	0.2084	0.063	0.9975	0.3345	-0.2638	-0.5993	0.1317	-0.3347	-0.141	-0.2092	-0.7995	-0.0414	0.3615	-0.1055	0.0217	0.5016	0.1553	0.4592	-6.057	-8.928	80.197
7	0.4513	-0.5482	0.2267	0.5882	-0.1521	0.2989	-0.0341	0.481	0.0457	-0.3581	0.1251	0.3746	0.2246	-0.1255	0.0007	0.3603	-0.0251	-0.042	0.3801	0.026	0.3191	-3.761	-33.68	11.863
8	0.5611	-0.1535	-0.3552	0.8231	-0.0106	0.241	-0.0016	-0.1431	0.2037	-0.0921	-0.1679	0.2444	-0.1314	-0.2069	-0.0002	0.2534	-0.0085	-0.0246	0.3433	0.029	0.3405	-1.88	-26.543	22.701
9	0.685	-0.7659	-0.3999	0.7791	-0.089	0.8464	0.0801	-0.6226	-0.2034	0.0088	-0.065	-0.1247	0.2029	-0.0425	-0	0.4235	-0.0274	-0.0322	0.4525	0.0483	0.4029	14.127	-33.202	42.138
10	1.3398	0.4792	0.5346	0.8278	-0.3261	1.8776	-0.1502	-0.4159	-0.0155	0.0464	0.1208	0.0592	0.0137	-0.0901	0.0001	0.3688	-0.0198	0.0309	0.3421	-0.0237	0.3681	6.295	-27.065	40.006
11	0.6382	0.0067	0.3579	0.0144	0.0457	0.1115	0.0154	-0.3733	0.6524	0.1108	0.0093	0.1905	-0.1742	-0.0418	0.0045	0.3559	-0.0307	0.0122	0.1633	-0.0279	0.2583	9.193	-20.056	25.078
12	0.6862	0.3148	0.5426	0.8052	1.2649	1.6681	-0.1124	0.254	-0.3085	0.0376	0.257	-0.2609	0.089	0.5227	-0	0.3065	-0.005	-0.0107	0.3302	-0.0092	0.3985	10.544	-31.831	25.304
13	0.7817	-0.0515	0.1608	0.7611	0.1465	0.7351	-0.2411	0.6225	-0.4713	-0.2393	-0.1522	-0.3608	0.0821	0.1024	-0.007	0.2949	-0.0595	0.0957	0.4322	0.0598	0.5227	5.338	-29.871	18.645
14	0.3164	-0.0413	0.2553	0.5005	-0.1879	0.2826	-0.0133	0.1371	-0.3186	-0.2186	0.0036	-0.0434	0.1753	0.0956	-0.0005	0.3199	-0.0224	-0.0516	0.3969	-0.0704	0.4144	4.059	-39.472	16.616
15	1.0854	0.7762	-0.1727	0.7349	-0.3993	1.533	-0.1622	-0.5372	-0.1109	0.3556	0.1331	0.3043	-0.8672	-0.0973	-0.0392	0.3816	0.0002	-0.0184	0.6403	-0.0436	0.3527	12.253	4.504	35.38
16	0.5245	0.1578	0.3307	0.7732	0.2717	0.5507	-0.1279	0.201	-0.0046	-0.1322	-0.0642	0.3851	0.1439	-0.3325	-0.0179	0.2537	-0.0874	0.0298	0.3162	0.0167	0.3486	14.64	-1.006	23.178
17	1.5176	-0.3477	-0.0395	0.6138	-0.6282	0.4642	-0.3216	0.2257	0.5535	-0.0778	0.1069	-0.4234	-0.0066	0.057	0	0.433	-0.0347	-0.0755	0.3779	0.0372	0.3901	30.217	9.95	6.491
18	1.8799	-0.1525	-0.3806	1.198	0.6297	2.3533	-0.0467	0.1401	0.0517	-0.138	-0.0187	0.0799	0.0009	0.0265	-0.0001	0.2925	-0.0081	-0.0194	0.1919	0.0204	0.257	23.49	0.128	14.473
19	0.7858	0.2318	-1.0395	0.7914	-0.4556	1.2562	-0.499	-0.7742	0.7173	0.5108	0.1684	-0.3534	0.0431	0.0353	-0.0157	0.292	-0.0137	-0.045	0.308	0.0066	0.4013	21.409	1.673	28.038
20	0.4379	0.2876	-0.2135	0.3153	-0.4856	0.9556	-0.0024	-0.0877	0.3572	0.6543	-0.286	-0.1368	-0.5194	0.4823	-0.0204	0.3933	-0.0064	-0.042	0.3705	-0.1353	0.3596	20.072	10.757	31.195
21	1.1737	0.1149	0.6007	0.2332	0.4243	0.704	-0.0984	0.9884	0.7888	-0.3565	0.0577	0.3951	-0.0254	0.883	-0.0049	0.4875	0.0934	0.0122	0.7743	0.1987	0.4806	20.174	26.471	62.947
22	0.4141	0.2744	-0.0317	0.3865	0.6657	0.6336	-0.2409	-0.1081	-0.0562	0.3529	0.1693	-0.1817	0.4302	0.3886	-0.0003	0.3158	0.0182	0.0698	0.3606	-0.0521	0.2921	15.804	23.825	79.09
23	2.5343	1.4506	0.4398	0.9564	0.5818	1.3969	-0.1933	-1.001	0.7143	-0.7018	-0.7297	0.1387	-0.4348	-0.3114	-0.2849	0.5465	-0.014	-0.0017	0.8144	-0.1489	0.5206	2.76	40.279	93.675
24	0.07	0.0884	0.1049	0.1448	0.0918	0.1969	-0.1595	0.8158	0.5683	-0.6584	-0.5173	0.1396	-0.704	0.0539	-0.0102	0.4965	-0.0428	0.0655	0.559	-0.0515	0.6251	2.015	40.003	87.114
25	2.2099	0.2079	0.0988	1.489	-0.0615	2.0942	0.0044	0.03	0.2321	0.0951	-0.0369	0.1062	0.2597	-0.242	0.0002	0.3313	-0.0098	0.0486	0.4067	-0.0542	0.3612	9.546	26.715	84.847
26	0.7104	-0.3901	-0.6551	0.8662	0.0191	0.7239	-0.6283	0.8717	0.5208	-0.942	0.5378	0.0296	0.1216	0.2529	-0.0043	0.3584	-0.0292	-0.0121	0.4179	0.0769	0.3941	11.722	26.045	71.169
27	1.068	0.0713	-0.1108	1.3395	1.3497	1.4743	0.0646	1.1405	1.3567	-1.2337	-0.6202	0.1828	-1.1636	-0.5043	-0.1264	0.4554	0.0339	-0.105	0.7235	0.2833	0.5411	13.036	34.658	66.54

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 38:60 )	A	38 - 60
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 61:105 )	A	61 - 105
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 106:131 )	A	106 - 131
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 132:239 )	A	132 - 239
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 240:261 )	A	240 - 261
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 262:280 )	A	262 - 280
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 38:60 )	B	38 - 60
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 61:86 )	B	61 - 86
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 87:117 )	B	87 - 117
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 118:177 )	B	118 - 177
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 178:196 )	B	178 - 196
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 197:239 )	B	197 - 239
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 240:254 )	B	240 - 254
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 255:280 )	B	255 - 280
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 38:60 )	C	38 - 60
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 61:87 )	C	61 - 87
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 88:131 )	C	88 - 131
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 132:239 )	C	132 - 239
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 240:254 )	C	240 - 254
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 255:280 )	C	255 - 280
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 36:60 )	D	36 - 60
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 61:95 )	D	61 - 95
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 96:117 )	D	96 - 117
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 118:131 )	D	118 - 131
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 132:239 )	D	132 - 239
26	X-RAY DIFFRACTION	26	( CHAIN D AND RESID 243:254 )	D	243 - 254
27	X-RAY DIFFRACTION	27	( CHAIN D AND RESID 255:280 )	D	255 - 280

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About Yorodumi

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Yorodumi