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- PDB-9h15: Crystal structure of OXA-163 in complex with nacubactam -

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Basic information

Entry
Database: PDB / ID: 9h15
TitleCrystal structure of OXA-163 in complex with nacubactam
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL 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
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-OP0 / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsHoff, J.F. / Goudar, K.E. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)R102376-101 United Kingdom
CitationJournal: 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
DepositionOct 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,29516
Polymers55,7392
Non-polymers1,55614
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-10 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.623, 79.043, 126.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase


Mass: 27869.543 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 , 7 types, 205 molecules

#2: 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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.8 / Details: 0.1 M Tris pH 8.8, 40% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.18→52.66 Å / Num. obs: 37053 / % possible obs: 98.7 % / Redundancy: 14.1 % / Biso Wilson estimate: 34.99 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.141 / Net I/σ(I): 5.1
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3661 / CC1/2: 0.327 / Rpim(I) all: 1.171 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→52.66 Å / SU ML: 0.2778 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0944
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.243 1881 5.08 %
Rwork0.1963 35172 -
obs0.1987 37053 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.61 Å2
Refinement stepCycle: LAST / Resolution: 2.18→52.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 96 191 4197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734131
X-RAY DIFFRACTIONf_angle_d0.84235570
X-RAY DIFFRACTIONf_chiral_restr0.0521579
X-RAY DIFFRACTIONf_plane_restr0.0074707
X-RAY DIFFRACTIONf_dihedral_angle_d14.60641524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.240.33321450.31642647X-RAY DIFFRACTION98.03
2.24-2.310.33941290.29032685X-RAY DIFFRACTION98.32
2.31-2.380.32461670.27192626X-RAY DIFFRACTION98.35
2.38-2.460.31161390.25812694X-RAY DIFFRACTION98.75
2.46-2.560.30881540.23232641X-RAY DIFFRACTION98.73
2.56-2.680.25971330.22922692X-RAY DIFFRACTION98.74
2.68-2.820.25791460.20962703X-RAY DIFFRACTION98.85
2.82-30.26651620.19762687X-RAY DIFFRACTION99.2
3-3.230.24131330.18962728X-RAY DIFFRACTION99.24
3.23-3.550.23861400.16862728X-RAY DIFFRACTION99.31
3.55-4.070.21731440.16742603X-RAY DIFFRACTION94.4
4.07-5.130.19451430.15262807X-RAY DIFFRACTION99.7
5.13-52.660.20831460.19222931X-RAY DIFFRACTION99.58
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
18.7612514827-1.5516475270.433683023865.357638213921.209547372896.70643076499-0.0296725824620.543411255274-0.932231847414-0.0204133170813-0.1158079958330.3527987901810.854685932274-0.1308419133480.1324310514080.491278175077-0.0922919032932-0.01578884864770.295828288796-0.04323406206950.236476985211-27.6757195505-12.9698315788-10.1584762468
28.6958994484-0.6294425095112.489762072454.218272909530.561813066895.14228095891-0.09223432955090.26320621891-0.414648257097-0.3866733910750.09258978153560.06268210764790.702746906410.1381739739210.04932473727170.455447228937-0.02162888458950.03664044487350.3038710572760.03150868443810.218636740992-22.1553790339-8.89530896398-6.94186333441
31.968124071251.48947140082.443176497995.310430603442.584920544415.63630981786-0.3298530676050.1352264910150.139581183652-0.6749878998090.296412241825-0.06072236056-0.95413078316-0.0164152430470.05494252737420.256210653755-0.008116676745430.05244660258430.2441202400830.01452435748540.206932968722-24.78396634376.60515029275-4.17322622219
43.76295081150.1497403291692.614510838151.793313830721.03389981963.23702921523-0.505679815958-0.7720982787810.5876459268460.05798452597580.08645548636470.172753510432-0.6086821106-0.8214986929980.4587491898220.5335306861820.161798001031-0.001585449299340.387953663972-0.04083608074170.367842041957-31.881297870116.332484400713.5965642734
54.01093167648-4.53258090264-0.7969801057047.050855235331.361220680330.2677787760830.0424948893621-0.5222424341720.0710290892108-0.239871098236-0.3602508335990.348752867788-0.380412328827-1.194850156740.2442813313610.2786594892790.09195772308250.02555616531780.563775594788-0.05360906234430.256469779297-31.126200110410.093351311713.257287286
66.22083015772-0.735802006176-0.7556209659125.235455677220.1246103327723.05257653922-0.1941402999240.1774354378910.839957705706-0.2120419047530.17949503997-0.117059305887-1.24058194901-0.108635320870.007058920143720.6544025777580.0236890795764-0.1283528543610.2585033408880.01550261395630.299869719714-22.932325588919.30002046010.909807346455
70.9755612451291.018786061610.5098317561081.591326149620.5767762336384.22571970256-0.1014402749520.1404021634610.104803838187-0.2166034281010.0840973395347-0.0413562382304-0.602179533021-0.04602885275630.01701717899560.312422903070.0149493215613-0.008824401573130.248529589297-0.004024508414570.247735315892-19.79265809449.22112223541-1.52916932893
82.123894001390.390462871569-0.1615525216842.489995397341.158850406914.117640709630.03137550863830.0862716105738-0.02950208538860.0976242359942-0.08799818111630.1971806286110.365144353678-0.5333605591720.02943642085980.262234477686-0.04572722605330.01223813846070.2762835813360.02935268705140.240844265671-27.7869798383-5.57746480771.8391634727
94.28775228988-2.42302554698-0.7246786087928.656571850411.534367298876.23030455860.206602728495-0.291643608094-0.2325771002260.934174293148-0.3539755928530.3740071269940.000146982452283-0.5499412731020.1512009524510.310069016982-0.1321357473030.03248461893090.6138732797770.01661680257450.283646813087-28.9797177825-5.67133119341.886145887
104.27007525453-0.455717060351-1.165580327080.782389622981-0.8588018228135.19155643558-0.1587534716-0.37710630727-0.00766209850260.1490954350610.1649695586580.03789440306430.104618098892-0.0448141727994-0.01674283235960.299880714994-0.0395730002512-0.02650062790950.17145825597-0.08503802901850.237324610337-16.3466742847-3.0500710422135.3330521113
113.85151139452-0.374079687962-0.2676979385055.59117531676-0.6676996437333.848278366880.2434415792960.0925023500795-0.253493602732-0.123495739189-0.346846563733-0.2385341417060.7744499235450.6923645208280.09827647413690.3556481686320.115867808390.00554973645990.404957254227-0.02239177113740.209930421307-4.65329549951-13.30971047416.2844883313
122.002951068530.274232629144-0.3918168040571.39381815584-0.5746543681813.664332983410.114587536751-0.209264953202-0.09999216523320.0516630061889-0.0461235868195-0.1060267107730.1151493234770.226045711955-0.07399583303450.260186450844-0.00248576928021-0.02321901983650.213596004008-0.0229267491240.233248230208-13.1033265127-4.3037958547629.3692713445
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 23 through 38 )AA23 - 381 - 16
22chain 'A' and (resid 39 through 56 )AA39 - 5617 - 34
33chain 'A' and (resid 57 through 83 )AA57 - 8335 - 61
44chain 'A' and (resid 84 through 105 )AA84 - 10562 - 83
55chain 'A' and (resid 106 through 119 )AA106 - 11984 - 97
66chain 'A' and (resid 120 through 142 )AA120 - 14298 - 120
77chain 'A' and (resid 143 through 194 )AA143 - 194121 - 172
88chain 'A' and (resid 195 through 261 )AA195 - 261173 - 239
99chain 'B' and (resid 23 through 38 )BG23 - 381 - 16
1010chain 'B' and (resid 39 through 83 )BG39 - 8317 - 61
1111chain 'B' and (resid 84 through 119 )BG84 - 11962 - 97
1212chain 'B' and (resid 120 through 261 )BG120 - 26198 - 239

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