PDB-9h13: Crystal structure of OXA-163 apoenzyme

ID or keywords:

Entry

Database: PDB / ID: 9h13

Title

Crystal structure of OXA-163 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 / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Enterobacter cloacae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.44 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	9h13.cif.gz	273.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9h13.ent.gz	183.1 KB	Display	PDB format
PDBx/mmJSON format	9h13.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9h13_validation.pdf.gz	461.5 KB	Display	wwPDB validaton report
Full document	9h13_full_validation.pdf.gz	463.3 KB	Display
Data in XML	9h13_validation.xml.gz	29.1 KB	Display
Data in CIF	9h13_validation.cif.gz	41.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h1/9h13 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/9h13	HTTPS FTP

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Related structure data

Related structure data	9h11C 9h12C 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

56.2 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)	122.553, 122.553, 160.430
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-412- HOH
2	1	A-613- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Beta-lactamase Mass: 27912.545 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: blaOXA-163 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6KZJ2, beta-lactamase

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Non-polymers , 5 types, 537 molecules

#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: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.11 Å³/Da / Density % sol: 60.51 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Tris pH 9.0, 32% PEG 550

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 1.44→48.69 Å / Num. obs: 127598 / % possible obs: 99.9 % / Redundancy: 40.1 % / CC_1/2: 0.999 / R_pim(I) all: 0.03 / Net I/σ(I): 13.5
Reflection shell	Resolution: 1.44→1.49 Å / Redundancy: 38.9 % / Num. unique obs: 12442 / CC_1/2: 0.348 / R_pim(I) all: 1.665 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.44→48.69 Å / SU ML: 0.2215 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.2027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1859	6565	5.15 %
R_work	0.1683	121033	-
obs	0.1692	127598	99.8 %

Solvent computation

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

Displacement parameters

B_iso mean: 26.84 Å²

Refinement step

Cycle: LAST / Resolution: 1.44→48.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3940	0	24	532	4496

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0057	4255
X-RAY DIFFRACTION	f_angle_d	0.79	5779
X-RAY DIFFRACTION	f_chiral_restr	0.0798	600
X-RAY DIFFRACTION	f_plane_restr	0.0059	752
X-RAY DIFFRACTION	f_dihedral_angle_d	12.9392	1570

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 (%)
1.44-1.46	0.3879	187	0.368	3928	X-RAY DIFFRACTION	97.86
1.46-1.47	0.3372	212	0.3531	3971	X-RAY DIFFRACTION	99.1
1.47-1.49	0.3737	234	0.3478	3910	X-RAY DIFFRACTION	99.57
1.49-1.51	0.3761	214	0.3514	3963	X-RAY DIFFRACTION	99.5
1.51-1.53	0.3924	201	0.3828	4005	X-RAY DIFFRACTION	99.39
1.53-1.55	0.3925	216	0.3826	3997	X-RAY DIFFRACTION	99.74
1.55-1.57	0.3906	186	0.3555	3993	X-RAY DIFFRACTION	99.62
1.57-1.6	0.3258	226	0.3256	3965	X-RAY DIFFRACTION	99.86
1.6-1.62	0.3428	205	0.291	4003	X-RAY DIFFRACTION	99.81
1.62-1.65	0.2748	200	0.2586	3965	X-RAY DIFFRACTION	99.93
1.65-1.68	0.273	213	0.2295	4028	X-RAY DIFFRACTION	99.86
1.68-1.71	0.2173	214	0.2021	4026	X-RAY DIFFRACTION	99.93
1.71-1.74	0.19	220	0.1851	3981	X-RAY DIFFRACTION	99.98
1.74-1.78	0.2035	213	0.1758	4020	X-RAY DIFFRACTION	99.95
1.78-1.81	0.1816	226	0.167	3997	X-RAY DIFFRACTION	99.98
1.81-1.86	0.1975	251	0.1728	3993	X-RAY DIFFRACTION	100
1.86-1.9	0.2065	196	0.1805	4027	X-RAY DIFFRACTION	99.98
1.9-1.95	0.2105	230	0.1692	4004	X-RAY DIFFRACTION	99.95
1.95-2.01	0.1803	244	0.1483	3996	X-RAY DIFFRACTION	100
2.01-2.08	0.1894	235	0.1449	4040	X-RAY DIFFRACTION	99.98
2.08-2.15	0.172	213	0.1482	4036	X-RAY DIFFRACTION	100
2.15-2.24	0.1814	236	0.1476	4036	X-RAY DIFFRACTION	100
2.24-2.34	0.1782	255	0.1521	4001	X-RAY DIFFRACTION	100
2.34-2.46	0.1694	207	0.1543	4091	X-RAY DIFFRACTION	100
2.46-2.62	0.1803	213	0.1589	4083	X-RAY DIFFRACTION	99.98
2.62-2.82	0.1805	203	0.1577	4100	X-RAY DIFFRACTION	99.98
2.82-3.1	0.1772	228	0.1532	4102	X-RAY DIFFRACTION	100
3.1-3.55	0.145	224	0.1401	4137	X-RAY DIFFRACTION	100
3.55-4.47	0.1291	238	0.1258	4192	X-RAY DIFFRACTION	100
4.47-48.69	0.1681	225	0.1614	4443	X-RAY DIFFRACTION	99.98

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	3.37526703478	-0.522443791352	3.47396766053	2.9649168862	-0.613994465158	7.43655190546	0.105879883212	0.103011494986	-0.381333670947	0.187829662475	0.0352126630089	-0.14255687207	0.316699217026	0.268296380176	-0.1441480271	0.201212355955	-0.00824972533331	0.0369858818497	0.124984421959	-0.0174081096089	0.220495328382	-52.4643477351	-4.00747087836	-25.2032729198
2	0.621515305248	-0.326341085799	-0.229759555397	8.57063940556	0.132735977715	0.98512013802	-0.0074621516743	0.0132968529078	-0.0586422521249	0.15380157355	0.0134654893484	0.200666710499	0.0928685683151	-0.00378938391323	-0.00399684052633	0.152970990013	-0.0211497964162	0.000543890702949	0.153771131104	0.0102997895452	0.152610610948	-61.5671293029	10.7269424381	-17.0009608409
3	4.08525291214	0.057644479442	2.84375938041	1.5026596105	-0.678814918057	7.33118048071	-0.0229905976343	-0.271850147301	0.158311048522	0.285968675858	0.0318025397003	-0.0129001482996	-0.236779636171	-0.0460651510035	0.0196564572237	0.26504528998	-0.00083214732589	0.00975132668603	0.165101798195	-0.0152747624961	0.193161927306	-55.6351678449	28.7238468657	-8.91131779401
4	3.00329001873	-1.11279775958	-2.61231990747	6.22053900973	-0.551658894233	5.30044692972	-0.0819876174543	-0.0913695384305	-0.101079979285	0.105712032207	0.0110641287838	-0.0872852117805	-0.0486167867387	0.249905270605	0.0900483043576	0.181208697204	-0.0242865638532	-0.0298654602071	0.169981626281	0.0127366512698	0.184874268055	-50.4278324841	23.0249069586	-9.86220276664
5	4.05300441416	1.3022889223	3.85834914722	2.31452000494	2.11698494509	7.12453144613	-0.0868827399071	-0.196525810157	0.118595010454	-0.0262805131723	-0.0430038308201	0.15688168976	-0.349579325107	-0.474777610703	0.159925913377	0.144687062778	0.0170922750351	0.019683926541	0.14653305784	0.0352517820154	0.137978376491	-67.7176542975	22.1870242233	-13.9281820129
6	1.19429829877	0.349114707889	-0.696403938507	1.12200150338	-0.0877303196662	1.38790427564	-0.0930079190652	0.164942304697	0.00959689660368	-0.00704368090493	0.0911104873784	0.070274188084	0.120280987185	-0.193877524675	-0.000315423120036	0.165197088046	-0.0269815035477	-0.010901843473	0.168680850974	0.00529683714884	0.145792005008	-63.5276371997	14.422130364	-21.741870841
7	5.39932200684	1.1152881435	-2.98787372924	3.46164404286	-1.71886214737	7.28023048201	-0.236258575841	-0.333408823173	-0.196477700395	0.0840328690741	0.0543021065036	-0.153474278424	0.315449577078	0.155650208875	0.206675325216	0.165700015559	-0.00639992891707	-0.0126857506526	0.115938860449	0.0131695729567	0.16663232761	-48.0261879593	12.1603197873	-19.1283477825
8	2.01272320979	0.462585030965	-0.765875244488	2.9112624147	-0.918588893602	5.2915577686	-0.0637853673169	-0.0696946491847	-0.174898686283	0.134158033541	0.0485626547955	-0.309272128923	0.229513137616	0.217216641634	0.0255668867979	0.180735330137	-0.0142015073246	-0.0131900271179	0.122433977404	0.00104003135167	0.197199955012	-48.0247732174	4.51450203332	-20.2723998527
9	4.58330201745	-4.28136792482	-2.54252970432	7.4830975603	5.01205045101	5.13688278409	0.0193595770001	-0.242205927979	0.115702601485	0.134601641611	0.28590264773	-0.761247590146	0.0105153385358	0.577760813667	-0.337604327901	0.209771171462	-0.0798418766048	-0.0442378973059	0.320359865114	0.0440213224561	0.362055867629	-22.2977839756	37.4780757856	-21.1440248032
10	1.37401419014	0.731646069093	0.780478386825	1.17261795308	0.233448116673	2.17790947637	-0.0461908037088	0.0248232850898	0.0351171435491	0.0909486997004	-0.0138593491731	-0.197340541627	-0.157657215384	0.25387493028	0.0624970137067	0.180334819951	-0.0324340459661	-0.025425083444	0.148984192692	0.02608518227	0.207010927098	-32.8165104511	36.2672551791	-31.2621706667
11	2.32891185096	-1.79011698838	-0.24759247592	3.71687672443	0.412096191086	2.47251646534	0.045261001591	0.06555519397	-0.115555110706	-0.0838383996265	-0.0553536820627	-0.0795874104368	0.253013678016	-0.0418947652792	0.00719042278512	0.1968949693	-0.0462525921512	0.00126994681224	0.169664847413	0.00301971764119	0.211906325461	-41.5033214972	18.2558485892	-44.9286932299
12	1.3907194219	-0.438319860402	0.174579538994	4.18062684061	1.28459702233	2.55783194621	0.000822554314939	0.100892910718	0.094268466569	-0.191960698029	0.00347389990982	-0.0984057591205	-0.1957177849	0.0386164684819	-0.00346592000357	0.144217976703	-0.0398137034501	0.00588832135231	0.148090292816	0.028453088237	0.147350605167	-41.7897270844	36.2377660839	-47.2452020421
13	2.53622046051	0.978957888635	-1.22554346345	1.18198235851	-0.783282298747	2.01787884953	0.0496368967304	0.0542090968578	0.117025753834	0.0658563570998	0.00466477359927	-0.0183663152189	-0.149616080698	0.0042331865994	-0.0666083556841	0.156917880073	-0.0161155442554	-0.0164586681945	0.131389106914	0.015917792053	0.155709710651	-42.0372866831	35.5821857356	-34.8301346151
14	2.03293964494	0.674763813157	-0.062901676247	1.92848337754	-0.441704271719	2.0429650497	0.0112286420533	-0.0221802563242	-0.16081086988	0.0404151378153	-0.0898770045162	-0.298464083983	0.0479512084032	0.285918645291	0.0799954966717	0.149056004925	-0.0203394363354	-0.0302714926079	0.180564540394	0.0411174331525	0.219296855257	-30.9841365833	27.2348663737	-26.8605079925

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 58 )	A	A	21 - 58	1 - 38
2	2	chain 'A' and (resid 59 through 82 )	A	A	59 - 82	39 - 62
3	3	chain 'A' and (resid 83 through 102 )	A	A	83 - 102	63 - 82
4	4	chain 'A' and (resid 103 through 119 )	A	A	103 - 119	83 - 99
5	5	chain 'A' and (resid 120 through 141 )	A	A	120 - 141	100 - 121
6	6	chain 'A' and (resid 142 through 194 )	A	A	142 - 194	122 - 174
7	7	chain 'A' and (resid 195 through 214 )	A	A	195 - 214	175 - 194
8	8	chain 'A' and (resid 215 through 261 )	A	A	215 - 261	195 - 241
9	9	chain 'B' and (resid 21 through 38 )	B	E	21 - 38	1 - 18
10	10	chain 'B' and (resid 39 through 83 )	B	E	39 - 83	19 - 63
11	11	chain 'B' and (resid 84 through 119 )	B	E	84 - 119	64 - 99
12	12	chain 'B' and (resid 120 through 155 )	B	E	120 - 155	100 - 135
13	13	chain 'B' and (resid 156 through 194 )	B	E	156 - 194	136 - 174
14	14	chain 'B' and (resid 195 through 261 )	B	E	195 - 261	175 - 241

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 537 molecules

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Experimental details

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Experiment

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Sample preparation

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Processing

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-Non-polymers , 5 types, 537 molecules

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 537 molecules

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