PDB-9h12: Crystal structure of OXA-48 in complex with nacubactam

ID or keywords:

Entry

Database: PDB / ID: 9h12

Title

Crystal structure of OXA-48 in complex with nacubactam

Components

Beta-lactamase

Keywords

ANTIMICROBIAL PROTEIN / antibiotic resistance / beta lactamase / class D / DBO

Function / homology

Function and homology information

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

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.51 Å

Authors

Hoff, J.F. / Goudar, K.E. / Hinchliffe, P. / Spencer, J.

Funding support

United Kingdom, 1items

Citation

Journal: Rsc Med Chem / Year: 2025
Title: Electrostatic interactions influence diazabicyclooctane inhibitor potency against OXA-48-like beta-lactamases.
Authors: Hoff, J.F. / Goudar, K.E. / Calvopina, K. / Beer, M. / Hinchliffe, P. / Shaw, J.M. / Tooke, C.L. / Takebayashi, Y. / Cadzow, A.F. / Harmer, N.J. / Mulholland, A.J. / Schofield, C.J. / Spencer, J.

History

Deposition	Oct 9, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 3, 2025	Provider: repository / Type: Initial release
Revision 1.1	Sep 24, 2025	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9h12.cif.gz	231.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9h12.ent.gz	185.9 KB	Display	PDB format
PDBx/mmJSON format	9h12.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9h12_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	9h12_full_validation.pdf.gz	1.4 MB	Display
Data in XML	9h12_validation.xml.gz	29.6 KB	Display
Data in CIF	9h12_validation.cif.gz	39.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h1/9h12 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/9h12	HTTPS FTP

-
Related structure data

Related structure data	9h11C 9h13C 9h14C 9h15C 9h16C 9h17C 9h18C 9hpvC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	121.759, 121.759, 159.842
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-409- HOH
2	1	A-477- HOH
3	1	A-537- HOH

-
Protein , 1 types, 2 molecules AB

#1: Protein	Beta-lactamase Mass: 28338.115 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: bla OXA-48, bla_4, blaOXA-48, AI2879V1_5232, GJJ21_26815, KPE71T_00045, SAMEA3727706_05517 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase

-
Non-polymers , 9 types, 362 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-OP0 / (2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide Mass: 326.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₈N₄O₇S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#8: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#9: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.02 Å³/Da / Density % sol: 59.24 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.8 / Details: 0.1 M Tris pH 8.8, 50% PEG 400

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 11, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.51→60.88 Å / Num. obs: 109282 / % possible obs: 100 % / Redundancy: 39.5 % / CC_1/2: 0.999 / R_pim(I) all: 0.047 / Net I/σ(I): 11.3
Reflection shell	Resolution: 1.51→1.56 Å / Redundancy: 33.5 % / Num. unique obs: 10755 / CC_1/2: 0.327 / R_pim(I) all: 0.956 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1-4487	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.51→60.88 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1924	5513	5.04 %
R_work	0.1731	-	-
obs	0.174	109282	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.51→60.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4000	0	217	329	4546

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4439
X-RAY DIFFRACTION	f_angle_d	0.837	5954
X-RAY DIFFRACTION	f_dihedral_angle_d	13.544	1669
X-RAY DIFFRACTION	f_chiral_restr	0.058	607
X-RAY DIFFRACTION	f_plane_restr	0.006	753

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 (%)
1.51-1.53	0.3638	179	0.3378	3417	X-RAY DIFFRACTION	100
1.53-1.55	0.3427	180	0.323	3392	X-RAY DIFFRACTION	100
1.55-1.56	0.3128	170	0.3049	3417	X-RAY DIFFRACTION	100
1.56-1.58	0.325	182	0.2938	3432	X-RAY DIFFRACTION	100
1.58-1.6	0.3091	171	0.2663	3394	X-RAY DIFFRACTION	100
1.6-1.63	0.2477	185	0.2562	3416	X-RAY DIFFRACTION	100
1.63-1.65	0.2715	185	0.2485	3411	X-RAY DIFFRACTION	100
1.65-1.67	0.2736	172	0.2379	3442	X-RAY DIFFRACTION	100
1.67-1.7	0.2324	179	0.227	3387	X-RAY DIFFRACTION	100
1.7-1.73	0.2651	176	0.2197	3422	X-RAY DIFFRACTION	100
1.73-1.76	0.255	209	0.2127	3391	X-RAY DIFFRACTION	100
1.76-1.79	0.2421	182	0.2086	3443	X-RAY DIFFRACTION	100
1.79-1.82	0.2273	196	0.1996	3396	X-RAY DIFFRACTION	100
1.82-1.86	0.2195	190	0.1939	3420	X-RAY DIFFRACTION	100
1.86-1.9	0.2392	178	0.1993	3458	X-RAY DIFFRACTION	100
1.9-1.95	0.2037	179	0.1773	3411	X-RAY DIFFRACTION	100
1.95-2	0.1856	161	0.1623	3471	X-RAY DIFFRACTION	100
2-2.05	0.1612	186	0.1485	3438	X-RAY DIFFRACTION	100
2.05-2.11	0.168	179	0.151	3442	X-RAY DIFFRACTION	100
2.11-2.18	0.1661	203	0.1478	3433	X-RAY DIFFRACTION	100
2.18-2.26	0.1579	183	0.1473	3457	X-RAY DIFFRACTION	100
2.26-2.35	0.1701	167	0.1484	3484	X-RAY DIFFRACTION	100
2.35-2.45	0.1741	209	0.1462	3447	X-RAY DIFFRACTION	100
2.45-2.58	0.1803	193	0.1489	3461	X-RAY DIFFRACTION	100
2.58-2.74	0.1734	182	0.1541	3492	X-RAY DIFFRACTION	100
2.74-2.96	0.1795	171	0.1483	3521	X-RAY DIFFRACTION	100
2.96-3.25	0.1662	194	0.1485	3507	X-RAY DIFFRACTION	100
3.25-3.72	0.1565	197	0.1472	3546	X-RAY DIFFRACTION	100
3.72-4.69	0.1587	178	0.1449	3616	X-RAY DIFFRACTION	100
4.69-60.88	0.2083	197	0.1951	3805	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	1.959	0.8608	0.2526	4.374	2.7195	5.5326	-0.0034	-0.1421	0.3447	-0.1991	0.2017	-0.3162	-0.5597	0.672	-0.2303	0.1585	-0.0728	-0.0354	0.2276	0.0074	0.278	31.8181	-40.0888	3.2161
2	3.2277	0.9921	1.3293	4.6474	4.1957	8.0908	0.085	-0.0461	0.1905	-0.0018	-0.0792	-0.1469	-0.1424	-0.0311	-0.0423	0.0712	-0.0318	0.0007	0.1127	0.0287	0.1465	27.8145	-45.1652	0.3869
3	6.718	3.8589	0.1245	3.3967	-0.2336	0.68	0.029	-0.0186	-0.1314	0.0426	-0.0236	-0.1353	0.0017	0.1132	-0.0045	0.0739	0.0041	-0.0096	0.1097	-0.0004	0.0735	21.3635	-58.1857	9.4182
4	2.5119	-2.2322	-1.2246	3.0173	2.4755	9.0641	-0.1422	-0.2502	-0.0506	0.5852	0.0601	0.2434	0.0419	-0.3318	0.0981	0.2481	-0.0461	0.0467	0.1819	0.0281	0.1819	2.3846	-61.7847	17.6138
5	6.2736	1.4465	2.8119	4.3992	-2.188	3.6165	-0.0711	-0.1584	0.1368	0.3989	-0.0266	0.2582	-0.0642	-0.3348	0.0887	0.1163	0.0142	0.039	0.1316	-0.0315	0.1371	4.4952	-54.5194	16.772
6	6.8503	-2.4482	-5.1258	2.8627	1.1655	4.8907	-0.1873	-0.1047	-0.2269	0.1767	0.0591	0.0066	0.2906	0.0353	0.1234	0.1175	-0.0222	-0.0432	0.1077	-0.0021	0.1119	14.8149	-69.0728	12.5437
7	2.0869	-0.1884	0.8401	1.1549	-0.7457	1.8832	0.0406	0.0811	-0.0893	-0.0162	-0.0475	-0.037	0.0748	0.1577	0.0062	0.0794	-0.0013	0.0087	0.097	-0.0145	0.0921	18.9908	-61.5861	5.326
8	3.1823	-0.0354	1.5893	1.0734	-0.1787	4.4651	-0.007	-0.0909	0.1769	0.1022	-0.0113	-0.0099	-0.1788	0.1319	0.0396	0.0886	-0.0208	-0.0102	0.0812	-0.0211	0.1228	18.1256	-47.514	7.1821
9	3.0981	1.0208	-1.0269	3.2696	-2.8494	8.1331	-0.0171	-0.1283	0.3796	0.0398	-0.0801	0.1115	-0.5731	0.0761	0.0672	0.1628	-0.0229	-0.0321	0.1164	-0.053	0.2257	20.0552	-38.5128	7.6453
10	4.2852	3.7402	-3.4713	7.4786	-4.4543	4.0076	0.2724	0.0292	0.4239	0.6232	0.0702	0.4436	-0.5474	-0.2617	-0.3436	0.2085	0.089	-0.0087	0.2427	-0.0365	0.2266	-21.4475	-37.5496	5.3983
11	3.5317	-0.5293	-0.3669	8.429	-3.5751	4.1029	0.0153	-0.2315	0.0827	0.1657	-0.1263	0.1522	-0.1798	-0.1761	0.0743	0.0903	0.0357	0.0053	0.2014	-0.0659	0.1509	-18.1779	-43.3128	3.8982
12	2.3785	-0.2361	-0.2143	1.238	-0.0142	1.769	0.0793	0.1109	0.1328	-0.1839	-0.053	-0.0759	-0.0957	0.0249	-0.0269	0.0984	0.007	-0.009	0.1134	0.0077	0.1007	-4.2143	-47.7666	-16.1934
13	2.0559	-2.8981	2.0061	4.9534	-1.651	5.326	-0.0252	0.0862	0.1758	-0.0797	-0.1964	-0.311	-0.0244	0.2863	0.2155	0.0919	-0.0208	0.0139	0.1559	0.0138	0.1903	4.6455	-42.1409	-15.9669
14	1.6187	0.871	-0.4765	2.7386	0.2513	2.5547	-0.0801	0.2197	0.0149	-0.1561	0.085	0.1357	0.0782	-0.1892	-0.0008	0.0723	0.0156	-0.029	0.1483	0.002	0.1231	-10.2442	-53.9326	-20.5831
15	3.2816	-1.5456	1.1655	1.847	-0.3603	2.1578	0.0388	-0.067	-0.1227	-0.047	0.0078	0.1327	0.0929	-0.1041	-0.0455	0.0703	-0.0101	0.001	0.1002	-0.0063	0.1076	-9.3086	-54.1874	-8.1884
16	4.2986	-1.6482	2.3028	3.255	-1.5385	4.1023	-0.0998	-0.0145	0.2601	-0.0329	0.0805	0.0084	-0.299	-0.1585	0.0896	0.0851	0.0173	0.0103	0.1021	-0.0061	0.1386	-6.7608	-40.4661	-7.081
17	2.6148	-1.2769	0.51	3.3015	-1.1656	3.1364	-0.0916	-0.1823	0.293	0.1219	0.0242	-0.0978	-0.3059	-0.0511	0.0718	0.0863	0.02	-0.0126	0.1364	-0.0419	0.1757	-10.0907	-39.0418	0.6437

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 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 82 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 83 through 102 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 103 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 243 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 244 through 265 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 21 through 38 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 39 through 58 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 59 through 102 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 103 through 119 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 120 through 155 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 156 through 194 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 195 through 218 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 219 through 265 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 9 types, 362 molecules

-
Details

-
Experimental details

-
Experiment

-
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

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 9 types, 362 molecules

-Details

-Experimental details

-Experiment

-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

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 9 types, 362 molecules

-
Details

-
Experimental details

-
Experiment

-
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

-
Yorodumi