PDB-8faj: OXA-48-NA-1-157 inhibitor complex

ID or keywords:

Entry

Database: PDB / ID: 8faj

Title

OXA-48-NA-1-157 inhibitor complex

Components

Beta-lactamase

Keywords

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

Function / homology

Function and homology information

penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Smith, C.A. / Stewart, N.K. / Toth, M. / Vakulenko, S.B.

Funding support

United States, 1items

Citation

Journal: Acs Infect Dis. / Year: 2023
Title: The C5 alpha-Methyl-Substituted Carbapenem NA-1-157 Exhibits Potent Activity against Klebsiella spp. Isolates Producing OXA-48-Type Carbapenemases.
Authors: Smith, C.A. / Stewart, N.K. / Toth, M. / Quan, P. / Buynak, J.D. / Vakulenko, S.B.

History

Deposition	Nov 28, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 11, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8faj.cif.gz	218.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8faj.ent.gz	173.5 KB	Display	PDB format
PDBx/mmJSON format	8faj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8faj_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	8faj_full_validation.pdf.gz	1.9 MB	Display
Data in XML	8faj_validation.xml.gz	23.4 KB	Display
Data in CIF	8faj_validation.cif.gz	32.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fa/8faj ftp://data.pdbj.org/pub/pdb/validation_reports/fa/8faj	HTTPS FTP

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Related structure data

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

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	73.564, 74.638, 97.608
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Beta-lactamase Mass: 30396.721 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase

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Non-polymers , 5 types, 283 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₇N₃O₆S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.2 Å³/Da / Density % sol: 44.21 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 mM CaCl2, 20 mM CoCl2, 20 mM CdCl2, 20% PEG 3350

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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 PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.75→37.32 Å / Num. obs: 54799 / % possible obs: 99.8 % / Redundancy: 7.6 % / CC_1/2: 0.999 / R_pim(I) all: 0.034 / R_rim(I) all: 0.094 / Net I/σ(I): 12.3
Reflection shell	Resolution: 1.75→1.78 Å / Num. unique obs: 2894 / CC_1/2: 0.747 / R_pim(I) all: 0.456

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→37.32 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2157	2636	4.82 %
R_work	0.1817	-	-
obs	0.1833	54676	99.67 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.75→37.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3974	0	61	272	4307

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4154
X-RAY DIFFRACTION	f_angle_d	1.207	5633
X-RAY DIFFRACTION	f_dihedral_angle_d	12.75	582
X-RAY DIFFRACTION	f_chiral_restr	0.064	599
X-RAY DIFFRACTION	f_plane_restr	0.007	721

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 (%)
1.75-1.78	0.4092	117	0.3301	2613	X-RAY DIFFRACTION	96
1.78-1.82	0.2473	157	0.2333	2681	X-RAY DIFFRACTION	100
1.82-1.85	0.2495	142	0.2106	2709	X-RAY DIFFRACTION	100
1.85-1.89	0.2431	138	0.2	2707	X-RAY DIFFRACTION	100
1.89-1.94	0.2568	139	0.2001	2732	X-RAY DIFFRACTION	100
1.94-1.99	0.2147	123	0.1901	2721	X-RAY DIFFRACTION	100
1.99-2.04	0.2584	116	0.184	2724	X-RAY DIFFRACTION	100
2.04-2.1	0.2321	166	0.1844	2697	X-RAY DIFFRACTION	100
2.1-2.17	0.2222	142	0.1823	2714	X-RAY DIFFRACTION	100
2.17-2.24	0.1984	126	0.1812	2738	X-RAY DIFFRACTION	100
2.25-2.33	0.2246	138	0.1803	2735	X-RAY DIFFRACTION	100
2.33-2.44	0.2455	147	0.1797	2729	X-RAY DIFFRACTION	100
2.44-2.57	0.1959	146	0.1832	2732	X-RAY DIFFRACTION	100
2.57-2.73	0.2335	125	0.1915	2750	X-RAY DIFFRACTION	100
2.73-2.94	0.2472	142	0.2054	2765	X-RAY DIFFRACTION	100
2.94-3.24	0.255	130	0.2047	2768	X-RAY DIFFRACTION	100
3.24-3.71	0.1833	135	0.1696	2797	X-RAY DIFFRACTION	100
3.71-4.67	0.1755	167	0.141	2781	X-RAY DIFFRACTION	100
4.67-37.32	0.1943	140	0.1707	2947	X-RAY DIFFRACTION	100

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	0.2849	-0.2131	-0.0584	0.2148	-0.0843	0.3034	0.149	-0.0363	-0.2174	-0.0801	-0.1378	-0.0664	0.3481	-0.1938	0.0017	0.2724	-0.0302	-0.0185	0.2685	0.054	0.3157	11.8338	-39.8746	-1.0336
2	1.0839	0.0547	-0.2277	1.5944	-0.1751	0.0657	-0.0499	-0.0355	-0.312	-0.039	-0.0788	-0.0902	0.1909	0.1218	-0.0363	0.1977	0.0086	0.0026	0.1509	0.0151	0.2015	8.9753	-37.2217	-6.5643
3	1.0305	0.0355	-0.451	0.3337	0.2381	0.5765	-0.0191	-0.0258	-0.1408	0.0151	0.0047	-0.0114	0.0664	-0.1518	-0	0.1574	-0.0177	-0.0022	0.1569	-0.002	0.1703	-3.3394	-24.7738	-5.3859
4	0.6486	0.2165	0.1067	0.6029	-0.0849	0.0541	0.0952	-0.1545	0.2924	0.0623	0.0629	-0.117	-0.4057	-0.0296	0.0002	0.3013	-0.0035	0.0168	0.2494	-0.0612	0.2696	-1.5565	-4.3708	-5.1285
5	0.2295	-0.014	-0.0763	0.1411	-0.2059	0.3596	0.0296	-0.0899	-0.0063	0.1308	-0.0523	-0.1888	-0.3669	0.2488	-0.0002	0.2423	-0.0373	0.0093	0.1698	-0.0117	0.1866	3.713	-7.4606	-5.73
6	0.4599	-0.2612	-0.1113	0.3323	-0.0295	0.2928	0.0715	-0.0962	-0.0451	-0.0997	-0.0069	-0.1105	-0.0803	-0.2053	0	0.1782	0.0072	0.0069	0.2015	0.0006	0.1807	-11.8009	-15.8013	-7.8417
7	1.2129	-0.2362	-0.2282	1.1743	-0.4091	0.5271	-0.0067	0.0866	-0.1521	-0.0452	-0.0289	0.0662	0.0992	-0.1155	-0	0.1516	-0.0074	-0.0107	0.1545	-0.0193	0.1534	-4.7704	-24.141	-10.5678
8	0.3252	0.1468	0.3168	1.1321	-0.3644	0.5646	-0.0893	-0.1866	-0.0216	0.092	-0.0124	-0.0715	-0.0021	0.1332	0	0.162	0.0061	-0.0214	0.179	0.0154	0.1443	7.7633	-21.4114	-3.8849
9	1.2734	0.1406	0.5021	1.5987	-0.17	0.2848	0.0779	-0.1133	-0.0499	-0.0096	-0.0224	-0.1374	0.0587	0.0602	0.0001	0.1355	-0.0055	-0.0168	0.1437	0.0093	0.1636	9.0127	-28.0533	-6.0859
10	0.7421	0.2822	0.2212	0.7851	-0.5265	0.6201	0.0124	0.0181	0.0261	0.0765	-0.0396	-0.2237	0.0514	0.1282	0.0002	0.1752	-0.019	-0.0218	0.2108	0.0305	0.1914	16.4423	-28.5411	-1.7334
11	1.228	-0.1036	-0.6108	1.3764	-0.1463	1.5829	0.0826	-0.052	0.4495	0.0707	-0.0617	-0.0235	-0.2833	0.2366	0.0002	0.2202	-0.0248	0.0186	0.1743	0.0268	0.2789	24.1311	0.5474	-26.208
12	0.2771	-0.2441	0.2569	0.3172	-0.06	0.456	-0.0807	0.1228	-0.3316	-0.1402	0.0559	-0.035	0.1572	-0.0488	-0.0001	0.2506	0.0214	0.0303	0.2151	-0.035	0.3384	18.6467	-26.9926	-34.7411
13	0.251	0.1653	-0.1067	0.1125	-0.0374	0.206	-0.0214	-0.1071	-0.2432	0.0826	0.0517	-0.0159	0.0213	0.0364	-0.0002	0.2472	0.0246	0.0261	0.1736	0.0065	0.267	19.9249	-24.5372	-29.1243
14	0.3827	0.2662	0.055	0.2321	-0.0687	0.2318	-0.1074	0.5521	0.0384	-0.3068	0.0548	0.0693	0.0753	-0.0514	-0.0013	0.2728	-0.0087	-0.0169	0.3836	0.0311	0.1757	14.2208	-14.1451	-42.4444
15	1.735	0.4739	-0.0068	0.6412	-0.1414	1.8117	0.0144	0.1517	0.1971	-0.0383	-0.0277	-0.0106	-0.1253	0.0232	0	0.1777	0.0173	0.0058	0.1485	0.0394	0.1845	17.7563	-7.6554	-29.7455
16	0.8169	0.4734	0.4825	0.9502	-0.3202	0.8463	0.1063	-0.2187	0.1547	0.1518	-0.079	-0.1786	-0.0251	0.3382	0.0005	0.2177	-0.029	-0.0168	0.2598	0.0156	0.2493	28.4711	-4.539	-19.6447

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 22 through 38 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 39 through 58 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 59 through 83 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 84 through 105 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 106 through 119 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 120 through 141 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 142 through 194 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 195 through 218 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 219 through 243 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 244 through 265 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 24 through 83 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 84 through 105 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 106 through 119 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 120 through 142 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 143 through 231 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 232 through 265 )

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