PDB-9h11: Crystal structure of OXA-48 apoenzyme

ID or keywords:

Entry

Database: PDB / ID: 9h11

Title

Crystal structure of OXA-48 apoenzyme

Components

Beta-lactamase

Keywords

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

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: 1.38 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

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Download

PDBx/mmCIF format	9h11.cif.gz	275.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9h11.ent.gz	183.5 KB	Display	PDB format
PDBx/mmJSON format	9h11.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9h11_validation.pdf.gz	436.6 KB	Display	wwPDB validaton report
Full document	9h11_full_validation.pdf.gz	436.8 KB	Display
Data in XML	9h11_validation.xml.gz	30.3 KB	Display
Data in CIF	9h11_validation.cif.gz	44.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h1/9h11 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/9h11	HTTPS FTP

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Related structure data

Related structure data	9h12C 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

57 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)	123.513, 123.513, 161.564
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22
Space group name Hall	P6₅2(x,y,z+1/12)
Symmetry operation	#1: x,y,z #2: x-y,x,z+5/6 #3: y,-x+y,z+1/6 #4: -y,x-y,z+2/3 #5: -x+y,-x,z+1/3 #6: x-y,-y,-z #7: -x,-x+y,-z+1/3 #8: -x,-y,z+1/2 #9: y,x,-z+2/3 #10: -y,-x,-z+1/6 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+5/6

Components on special symmetry positions

ID	Model	Components
1	1	A-417- HOH
2	1	A-664- HOH
3	1	A-668- HOH

#1: Protein	Beta-lactamase Mass: 28381.115 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
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 675 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 3.13 Å³/Da / Density % sol: 60.75 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 33% v/v PEG 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8622 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: 0.8622 Å / Relative weight: 1
Reflection	Resolution: 1.38→61.76 Å / Num. obs: 148214 / % possible obs: 100 % / Redundancy: 40.2 % / CC_1/2: 0.999 / R_pim(I) all: 0.055 / Net I/σ(I): 8.9
Reflection shell	Resolution: 1.38→1.4 Å / Redundancy: 41.1 % / Num. unique obs: 14595 / CC_1/2: 0.309 / R_pim(I) all: 1.02 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.38→61.76 Å / SU ML: 0.1504 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.4918
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1869	7303	4.93 %
R_work	0.1701	140911	-
obs	0.1709	148214	99.96 %

Solvent computation

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

Displacement parameters

B_iso mean: 19.53 Å²

Refinement step

Cycle: LAST / Resolution: 1.38→61.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4006	0	13	675	4694

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0054	4231
X-RAY DIFFRACTION	f_angle_d	0.7816	5742
X-RAY DIFFRACTION	f_chiral_restr	0.0774	598
X-RAY DIFFRACTION	f_plane_restr	0.0065	744
X-RAY DIFFRACTION	f_dihedral_angle_d	12.6057	1566

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 (%)
1.38-1.4	0.3312	262	0.3142	4595	X-RAY DIFFRACTION	99.86
1.4-1.41	0.307	235	0.3029	4659	X-RAY DIFFRACTION	99.94
1.41-1.43	0.2912	227	0.2996	4617	X-RAY DIFFRACTION	99.88
1.43-1.45	0.288	252	0.2927	4624	X-RAY DIFFRACTION	99.9
1.45-1.47	0.3213	225	0.275	4654	X-RAY DIFFRACTION	99.92
1.47-1.49	0.2854	245	0.2694	4645	X-RAY DIFFRACTION	99.92
1.49-1.51	0.2628	239	0.2614	4646	X-RAY DIFFRACTION	99.98
1.51-1.53	0.269	238	0.2435	4624	X-RAY DIFFRACTION	99.98
1.53-1.55	0.2608	265	0.2384	4626	X-RAY DIFFRACTION	100
1.55-1.58	0.2189	256	0.2204	4631	X-RAY DIFFRACTION	99.96
1.58-1.61	0.2536	252	0.2141	4636	X-RAY DIFFRACTION	99.92
1.61-1.64	0.2094	234	0.203	4647	X-RAY DIFFRACTION	99.96
1.64-1.67	0.238	220	0.1994	4708	X-RAY DIFFRACTION	99.98
1.67-1.7	0.2016	236	0.1904	4631	X-RAY DIFFRACTION	99.98
1.7-1.74	0.2256	243	0.188	4702	X-RAY DIFFRACTION	100
1.74-1.78	0.1988	229	0.1825	4662	X-RAY DIFFRACTION	99.92
1.78-1.82	0.1929	232	0.1765	4679	X-RAY DIFFRACTION	100
1.82-1.87	0.1863	239	0.1776	4672	X-RAY DIFFRACTION	99.98
1.87-1.93	0.1822	242	0.1718	4686	X-RAY DIFFRACTION	99.98
1.93-1.99	0.1636	238	0.1561	4700	X-RAY DIFFRACTION	100
1.99-2.06	0.1608	249	0.1505	4691	X-RAY DIFFRACTION	100
2.06-2.14	0.1836	231	0.1472	4701	X-RAY DIFFRACTION	100
2.14-2.24	0.1601	223	0.1463	4725	X-RAY DIFFRACTION	100
2.24-2.36	0.1975	253	0.1552	4714	X-RAY DIFFRACTION	100
2.36-2.51	0.1622	236	0.1593	4755	X-RAY DIFFRACTION	100
2.51-2.7	0.1793	282	0.1628	4720	X-RAY DIFFRACTION	99.98
2.7-2.97	0.1684	275	0.156	4739	X-RAY DIFFRACTION	99.98
2.97-3.4	0.1507	255	0.1508	4806	X-RAY DIFFRACTION	100
3.4-4.29	0.1679	244	0.1325	4874	X-RAY DIFFRACTION	100
4.29-61.76	0.1585	246	0.149	5142	X-RAY DIFFRACTION	99.94

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	1.90895127088	-0.100648957479	-1.65539868023	2.12695584432	2.11921999616	5.88283112097	0.187095656755	-0.173492393108	0.326876741901	-0.101375574505	0.0202936972981	-0.144174221847	-0.579921436555	0.342694131499	-0.252017888371	0.168012509211	-0.0566957897921	-0.0154991801749	0.179926559706	-0.000978034578545	0.235333824051	31.3945308965	-40.9013147196	3.10244482656
2	1.24532242771	0.40058839503	-0.347113014517	0.802244676043	-0.522793778578	0.767806272621	0.0351314340063	-0.0365896735931	0.0774548516734	0.0466397847744	-0.0485531489018	-0.0403059915999	-0.062228197622	0.0642047022078	0.0212439324753	0.0773429382656	-0.0120602876938	-0.00697759174164	0.128970347894	-0.0123872673175	0.105747706887	24.0120008574	-53.5253177467	4.84720104981
3	1.97046924948	-0.216663946696	-0.498501734668	3.03084670312	1.14923792847	2.94599717211	0.0288449640786	-0.278245180716	-0.0128705509108	0.244667908706	-0.0361947675266	0.040952748002	0.0409768249096	-0.188035887029	0.00931112628541	0.102724965963	-0.0087046360305	0.0065029709206	0.192776495081	-0.00204642737864	0.116529454306	3.64634822517	-59.3819677637	17.5861406895
4	3.65629910122	-1.73382022516	-3.64963987652	2.81409844569	1.667827872	5.44304276656	-0.0909630222297	-0.0523634901528	-0.205134566882	0.164012178067	-0.0172282880694	0.0227659520751	0.433693175082	-0.0607741362791	0.124815396225	0.110346295236	-0.035517585894	-0.0441855218329	0.124614914461	0.00576244601922	0.105704646414	14.8163552762	-70.2087674386	12.7795074908
5	1.180541444	-0.130709890533	0.704246610367	0.58210835956	-0.305133036903	1.69021775354	0.0515986315709	0.0466746400145	-0.0526066214954	-0.00147889027184	-0.0600114862606	-0.0358930211919	0.0821589763391	0.136902293798	0.00922118912804	0.0668583792855	-0.00441046474838	0.00166942008743	0.102062857135	-0.00460473837887	0.0909311747311	18.9309464106	-63.024504558	5.36269208535
6	2.34679156869	-0.738569421084	1.45003172196	1.4044409095	-1.0447122611	2.03135830805	-0.0763352315672	-0.0848912877138	0.157555412096	0.204103193658	-0.0833267188856	-0.0979044374099	-0.238770451324	0.124915664656	0.159681566783	0.0962604236181	-0.0287384334202	-0.0110503912841	0.124029196017	-0.0147982121332	0.112043772282	15.6888627204	-49.7132038947	10.1430041803
7	2.00233711918	0.0491674952908	1.31682043012	0.83289428643	-0.156703228618	4.0691854843	-0.0171424314465	-0.0235688164295	0.224306727442	0.0683251125916	-0.0437793594681	-0.0146822346251	-0.241602926745	0.0455352722083	0.0634879501193	0.0824663064708	-0.0234343588504	-0.00187341756814	0.11505242488	-0.0128638547483	0.141623783162	19.8206533207	-44.2694793602	6.0651861531
8	1.74329934579	1.79929288509	-1.74925649222	3.8273400959	-2.67836739901	3.12848760245	0.217909956154	-0.220533359962	0.469475588505	0.356885156251	0.0330950468571	0.422747524481	-0.488924049074	-0.143684262646	-0.266568472452	0.194720404842	0.0695130324941	0.0130677991774	0.23359163711	-0.0687926799534	0.258090560542	-21.6986903178	-38.8003600586	5.77405246327
9	2.86807972566	-1.01128527164	-0.165172538203	6.92635560444	-2.93801730258	3.72164253838	-0.0034400364967	-0.130434256692	0.0611960436758	0.123798231979	-0.0643753359972	0.151911357846	-0.225820772163	-0.194726513277	0.0415417533936	0.0960544000235	0.0197696467859	-0.00353372148319	0.181047324212	-0.0713387795601	0.141624549806	-18.4286451242	-44.7166789059	4.29978455584
10	1.71144797819	-0.263534712825	-0.204999030188	0.970079221112	0.196356156584	0.77246049723	0.0384483250884	0.0631075730935	0.146318230339	-0.115054275512	-0.0228435236203	-0.0711807570204	-0.10968649661	0.0176562674789	-0.0218532650755	0.0939641509921	0.0153051588595	-0.0055772440238	0.124973023769	0.0077964520376	0.0959495791733	-2.13143766696	-47.3349884739	-15.6757415281
11	2.47670094791	1.09534232991	-0.670826695284	1.72054876926	-0.443456826001	1.40991240102	0.0209498603005	0.217156924867	-0.0368294078634	-0.0771848626841	-0.0164112727585	0.0613360169802	0.023510554685	-0.129740856469	-0.00105185851628	0.0967548813644	0.0330703107766	-0.0153621626882	0.166899025316	-0.0188268767804	0.108237291908	-11.1596133781	-55.239245461	-20.3841322846
12	2.10986212207	-0.983637645021	0.873593588586	1.05358353067	-0.495157085977	1.11277267321	0.0405546742601	-0.0296581122165	-0.032160222922	-0.0287242259113	-0.0136905528641	0.0719683976713	0.0241280475303	-0.0825336898842	-0.0332252600297	0.0615474215859	-0.0021825854987	-0.00137811129512	0.124779548669	-0.0188581434312	0.0998356525976	-9.95748062231	-55.2175990936	-7.89405039469
13	1.84624020681	-0.50468986816	0.602271106384	1.05270483293	-0.225453036325	1.8743455371	-0.0254729548206	-0.0742497580389	0.255471802151	0.0109318984037	0.00647157206203	0.0136039535392	-0.194783782849	-0.069658345571	0.0281813163382	0.103318605193	0.0110250939092	-0.00251450923139	0.126109832623	-0.0313556241902	0.169497084451	-9.02377729932	-41.0606119019	-1.28874953652

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 21 through 38 )	A	A	21 - 38	1 - 18
2	2	chain 'A' and (resid 39 through 83 )	A	A	39 - 83	19 - 63
3	3	chain 'A' and (resid 84 through 119 )	A	A	84 - 119	64 - 99
4	4	chain 'A' and (resid 120 through 141 )	A	A	120 - 141	100 - 121
5	5	chain 'A' and (resid 142 through 194 )	A	A	142 - 194	122 - 174
6	6	chain 'A' and (resid 195 through 218 )	A	A	195 - 218	175 - 198
7	7	chain 'A' and (resid 219 through 265 )	A	A	219 - 265	199 - 245
8	8	chain 'B' and (resid 21 through 38 )	B	D	21 - 38	1 - 18
9	9	chain 'B' and (resid 39 through 58 )	B	D	39 - 58	19 - 38
10	10	chain 'B' and (resid 59 through 119 )	B	D	59 - 119	39 - 99
11	11	chain 'B' and (resid 120 through 155 )	B	D	120 - 155	100 - 135
12	12	chain 'B' and (resid 156 through 194 )	B	D	156 - 194	136 - 174
13	13	chain 'B' and (resid 195 through 265 )	B	D	195 - 265	175 - 245

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