PDB-9h16: Crystal structure of OXA-405 apoenzyme

ID or keywords:

Entry

Database: PDB / ID: 9h16

Title

Crystal structure of OXA-405 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

Serratia marcescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.56 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	9h16.cif.gz	271.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9h16.ent.gz	181.2 KB	Display	PDB format
PDBx/mmJSON format	9h16.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h1/9h16 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/9h16	HTTPS FTP

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Related structure data

Related structure data	9h11C 9h12C 9h13C 9h14C 9h15C 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

56.6 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)	122.081, 122.081, 159.119
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	B-423- HOH
2	1	B-601- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Beta-lactamase Mass: 27880.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: blaOXA-405 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F6P2I5, beta-lactamase

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Non-polymers , 6 types, 516 molecules

#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 507 / 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: 3.07 Å³/Da / Density % sol: 59.93 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 28% PEG 550

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 7, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.56→63.57 Å / Num. obs: 99172 / % possible obs: 100 % / Redundancy: 13.4 % / CC_1/2: 0.997 / R_pim(I) all: 0.053 / Net I/σ(I): 8
Reflection shell	Resolution: 1.56→1.59 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 9689 / CC_1/2: 0.348 / R_pim(I) all: 1.629 / % possible all: 100

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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: 1.56→61.04 Å / SU ML: 0.206 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.3536
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1929	5040	5.08 %
R_work	0.1747	94132	-
obs	0.1756	99172	99.79 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.23 Å²

Refinement step

Cycle: LAST / Resolution: 1.56→61.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3886	0	54	507	4447

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0064	4199
X-RAY DIFFRACTION	f_angle_d	0.8406	5682
X-RAY DIFFRACTION	f_chiral_restr	0.056	584
X-RAY DIFFRACTION	f_plane_restr	0.0063	733
X-RAY DIFFRACTION	f_dihedral_angle_d	12.9649	1551

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 (%)
1.56-1.58	0.3985	165	0.3572	3063	X-RAY DIFFRACTION	98.78
1.58-1.6	0.3523	175	0.3387	3035	X-RAY DIFFRACTION	99.32
1.6-1.62	0.3603	164	0.3215	3087	X-RAY DIFFRACTION	99.09
1.62-1.64	0.3109	169	0.3041	3082	X-RAY DIFFRACTION	99.54
1.64-1.66	0.3348	188	0.2838	3065	X-RAY DIFFRACTION	99.75
1.66-1.68	0.2573	156	0.2725	3078	X-RAY DIFFRACTION	99.66
1.68-1.7	0.2678	185	0.2615	3078	X-RAY DIFFRACTION	99.79
1.7-1.73	0.3015	157	0.2605	3130	X-RAY DIFFRACTION	99.88
1.73-1.76	0.2967	161	0.2501	3102	X-RAY DIFFRACTION	99.79
1.76-1.79	0.2677	147	0.2441	3105	X-RAY DIFFRACTION	99.91
1.79-1.82	0.2432	157	0.2452	3115	X-RAY DIFFRACTION	99.85
1.82-1.85	0.2674	159	0.245	3121	X-RAY DIFFRACTION	99.79
1.85-1.89	0.2751	163	0.2309	3090	X-RAY DIFFRACTION	99.91
1.89-1.92	0.2472	177	0.2153	3110	X-RAY DIFFRACTION	99.76
1.92-1.97	0.1922	169	0.1951	3124	X-RAY DIFFRACTION	99.97
1.97-2.01	0.2249	190	0.178	3096	X-RAY DIFFRACTION	99.94
2.01-2.06	0.1923	181	0.1626	3089	X-RAY DIFFRACTION	99.85
2.06-2.12	0.1706	162	0.1596	3147	X-RAY DIFFRACTION	100
2.12-2.18	0.1753	156	0.1633	3151	X-RAY DIFFRACTION	100
2.18-2.25	0.1825	185	0.1585	3104	X-RAY DIFFRACTION	99.97
2.25-2.33	0.1852	162	0.1648	3144	X-RAY DIFFRACTION	99.97
2.33-2.42	0.161	157	0.1645	3151	X-RAY DIFFRACTION	99.97
2.42-2.53	0.1738	170	0.1657	3156	X-RAY DIFFRACTION	99.91
2.53-2.67	0.1887	157	0.1632	3186	X-RAY DIFFRACTION	99.88
2.67-2.83	0.2171	165	0.1614	3172	X-RAY DIFFRACTION	99.97
2.83-3.05	0.1851	163	0.1607	3188	X-RAY DIFFRACTION	100
3.05-3.36	0.1663	165	0.1587	3194	X-RAY DIFFRACTION	100
3.36-3.85	0.1653	171	0.1434	3238	X-RAY DIFFRACTION	100
3.85-4.85	0.1314	174	0.1312	3274	X-RAY DIFFRACTION	100
4.85-61.04	0.1984	190	0.1809	3457	X-RAY DIFFRACTION	99.78

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	1.60509118308	0.489227898961	0.713617311813	4.6621695873	2.27952319982	3.87344676685	0.00732087672305	-0.105053567741	-0.64029478078	0.376901234914	0.332501328215	-0.198956142264	0.548508874426	0.246124023652	-0.331163781407	0.334987876203	0.121858766995	-0.00266923959134	0.361766571627	0.0875918826781	0.488325052049	20.9953077568	37.8489070093	5.66286211817
2	3.91284787571	-0.26699071642	0.201829377471	3.77013460123	0.491858751304	2.90449424004	0.110504039074	-0.171920817065	-0.159791306228	0.0725375970307	-0.226938041194	-0.313667122161	0.328863340793	0.192848782565	0.0868697500539	0.184109794923	0.0444511295993	0.00238216207618	0.30474730161	0.0795583192612	0.229934860234	17.8621884894	43.5872987371	4.36306019535
3	1.18984478549	0.456488977851	0.240599638116	0.960899375173	0.0252571990893	1.68116775563	-0.0195399720184	0.0744535529549	-0.0932613778026	-0.0699029310417	0.0185148836388	0.0721409102054	0.0894941754042	-0.0770077968235	-0.00239303559514	0.14330470171	0.0164277998653	0.0145498694932	0.188396262334	0.00454619046699	0.175174294455	1.44934167416	46.6906343709	-16.5360789882
4	2.80426394892	0.45244016361	3.90028615102	0.333741560129	0.530761168939	9.03181991366	-0.0389818141469	0.113233268699	0.0447718958166	-0.0860987590227	0.0789377422145	-0.161774728759	-0.409656576592	0.131293325045	-0.0344585029092	0.212655849903	0.00295477446533	0.0171533791835	0.226975578719	0.0248344617788	0.210597283272	12.1311540012	59.5593351024	-19.3377104006
5	1.23962215789	-0.0645261549592	-0.148418724733	0.88798147922	-0.135133048159	1.34335165635	0.0240316511066	0.0309583278426	-0.0173142928714	-0.031211804896	0.00599959652559	-0.092583036085	-0.0100738681002	0.112226629265	-0.0341929659851	0.15451381882	0.00930817479973	0.00493156811951	0.204511628965	0.0116925690052	0.188895332375	10.8937131766	53.6662700036	-10.6561048219
6	4.43059298384	0.185185296252	-0.6769773264	1.73831337426	-0.475112525052	2.82645948608	-0.0757695773959	0.0191347666987	-0.481707134666	-0.0109585139564	0.0729585269316	0.0302637605407	0.415340119346	0.278824772424	0.111757081883	0.176856432664	0.047849959558	0.00382975980395	0.186771665569	0.0150168041088	0.219208426839	3.36913854208	42.0629110206	-2.46618266018
7	2.60381405948	-0.0946138610346	-0.390485739018	1.61343117542	0.182425154485	2.82579399541	-0.0516932865657	-0.206593730255	-0.14519015026	0.0493057025063	0.0303722589363	-0.0785933553735	0.179200613029	0.223147552799	0.0236109238763	0.178467426053	0.033251495745	0.0146831075189	0.230919778966	0.0484990488122	0.217307138122	9.81012095614	44.5033011595	1.10609677623
8	3.42008477776	0.479437787955	0.721501060855	3.85676744667	0.108451323191	4.75151155057	-0.0719143908688	-0.201656158858	-0.500249925149	0.00637025532063	0.153259408413	0.113429323934	0.747431238714	-0.0546314090325	-0.111442694017	0.329913613303	0.0481702957648	0.0418446194735	0.301074515427	0.116489850434	0.460803758839	9.40154359358	35.3207052619	3.22237756139
9	1.9665202797	-0.184178655312	0.597363979901	3.01543404471	-1.87110094215	6.07637224236	0.156049070935	-0.175280639028	-0.357056541692	-0.132038470193	-0.0193648573406	0.359631248767	0.737301646033	-0.291358868713	-0.128320282079	0.261845598218	-0.0589651162942	0.000607816712812	0.281394153993	-0.0366068824807	0.467604147425	-31.9268730507	40.7953801907	3.45402149929
10	3.26009677092	0.782875270372	0.814881750923	1.63704804423	0.823974001488	1.08125580813	0.107948005955	0.0711364900162	-0.307926335762	0.0223397544863	-0.0770129541537	0.0997952568375	0.1143360057	-0.0877217961496	-0.00703398863723	0.146020877133	0.00373783413455	-0.0102677343566	0.187628639985	-0.00597798224947	0.17921400197	-24.5726871124	52.650039639	5.60656581266
11	1.82762092761	-0.822330163718	0.621342787207	2.30552130825	-0.386606705273	3.31454175422	0.0695660307397	-0.344333316518	0.0818096570271	0.312730437243	0.00110746965201	-0.0974780848973	0.0203063202559	0.200142805423	-0.0715857245082	0.2103008233	-0.0268305836994	-0.0042309518539	0.296776895924	0.00604814491745	0.229706444389	-3.19230459361	62.3661420256	17.8244685389
12	2.10336803365	0.489324930533	-0.436097969041	1.71760470958	0.539510536418	2.64853782528	-0.0777955683197	-0.115625381309	-0.088740856019	0.168779876496	-0.0580810766592	-0.0631028085812	0.0692389566119	0.449839920458	0.134924463253	0.19699982693	0.00709158965986	-0.00494311848306	0.254495726488	0.0325940479158	0.204980620682	-5.47298935044	55.0861522108	17.0003604921
13	1.83209010783	-0.0324648442641	-0.0497003310647	1.47642449598	-0.177304470129	2.49443997043	-0.0228269637934	-0.0228409329167	0.162939535809	0.064967381752	-0.0121568256162	0.115480949305	-0.30345743535	-0.0877011475339	0.025463593376	0.206468703288	-0.00620491444773	0.013296230734	0.184171173389	0.000955904021016	0.191973726108	-18.1170761923	68.9544805161	12.4083259625
14	2.39751816847	-0.132917428927	-0.819276094917	1.08323787397	0.415874505166	0.723544220014	0.140244692954	0.209454931938	0.0530553390904	-0.0919481481579	-0.106052865901	0.0219346216251	-0.0781463911389	-0.166456038418	-0.0327672372484	0.17785931224	0.0243579320426	-0.006944352114	0.235605711909	0.0148072939096	0.168743346546	-17.6546863764	60.5251366672	2.8912466316
15	3.78017351835	-0.486246473494	-0.502834126561	3.45862280726	0.158946529362	2.83116404175	-0.0186785085234	-0.200603859657	-0.211749112651	0.309357539892	-0.0642267648701	0.117526753824	0.102986290503	-0.227576072046	0.133406103908	0.152711126479	-0.0186497152535	0.0115101618573	0.217978848241	0.0152206801146	0.200490736037	-13.548572018	47.451070642	7.56817319044
16	3.98442444249	-1.07523237272	-0.249376258517	2.28848854753	0.54988432169	2.68943827073	-0.0112138557536	0.223728168015	-0.351429879215	0.00159500519961	-0.0742118050812	0.0836478396214	0.179498316975	-0.227910668855	0.123009813249	0.151960926955	-0.018352592058	-0.00572939606735	0.189303808875	-0.0166513093413	0.206482440943	-19.8633691617	47.4970166356	2.93107353921
17	5.74584420988	0.0634548004978	0.0747056263114	4.85680879617	-0.581962017967	4.35542052361	-0.0910597962179	-0.179510597737	-0.711537972882	0.562928348806	-0.142657558172	-0.166024568249	0.48145961737	-0.113030681196	0.254163969044	0.346808050638	-0.0324448766488	0.0420478736885	0.303634560344	0.0418966570574	0.488823896144	-20.7260063898	39.4697459505	7.7878107734

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 58 )	A	A	39 - 58	19 - 38
3	3	chain 'A' and (resid 59 through 130 )	A	A	59 - 130	39 - 110
4	4	chain 'A' and (resid 131 through 141 )	A	A	131 - 141	111 - 121
5	5	chain 'A' and (resid 142 through 194 )	A	A	142 - 194	122 - 174
6	6	chain 'A' and (resid 195 through 214 )	A	A	195 - 214	175 - 194
7	7	chain 'A' and (resid 215 through 236 )	A	A	215 - 236	195 - 216
8	8	chain 'A' and (resid 237 through 261 )	A	A	237 - 261	217 - 237
9	9	chain 'B' and (resid 21 through 38 )	B	C	21 - 38	1 - 18
10	10	chain 'B' and (resid 39 through 82 )	B	C	39 - 82	19 - 62
11	11	chain 'B' and (resid 83 through 102 )	B	C	83 - 102	63 - 82
12	12	chain 'B' and (resid 103 through 119 )	B	C	103 - 119	83 - 99
13	13	chain 'B' and (resid 120 through 155 )	B	C	120 - 155	100 - 135
14	14	chain 'B' and (resid 156 through 194 )	B	C	156 - 194	136 - 174
15	15	chain 'B' and (resid 195 through 214 )	B	C	195 - 214	175 - 194
16	16	chain 'B' and (resid 215 through 236 )	B	C	215 - 236	195 - 216
17	17	chain 'B' and (resid 237 through 261 )	B	C	237 - 261	217 - 237

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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

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 516 molecules

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-Protein , 1 types, 2 molecules AB

-Non-polymers , 6 types, 516 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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 516 molecules

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Details

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Experimental details

-
Experiment

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Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi