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- PDB-9h14: Crystal structure of OXA-163 in complex with avibactam -

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Basic information

Entry
Database: PDB / ID: 9h14
TitleCrystal structure of OXA-163 in complex with avibactam
Components(Beta-lactamase) x 2
KeywordsANTIMICROBIAL 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 / 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-NXL / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,2039
Polymers55,7822
Non-polymers1,4217
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-5 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.600, 122.600, 160.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(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
IDModelComponents
11A-413-

HOH

21A-576-

HOH

31A-585-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Beta-lactamase


Mass: 27912.545 Da / Num. of mol.: 1
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
#2: Protein Beta-lactamase


Mass: 27869.543 Da / Num. of mol.: 1
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 , 6 types, 412 molecules

#3: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Chemical ChemComp-A1IY4 / (2S,5R)-1-methanoyl-5-(oxidanylamino)piperidine-2-carboxamide / avibactam, reacted form


Mass: 187.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13N3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C18H38O10 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.56→106.2 Å / Num. obs: 101172 / % possible obs: 100 % / Redundancy: 38.7 % / CC1/2: 0.999 / Rpim(I) all: 0.031 / Net I/σ(I): 12.8
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 39.1 % / Num. unique obs: 4960 / CC1/2: 0.313 / Rpim(I) all: 0.899 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→64.03 Å / SU ML: 0.218 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.3352
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1843 5025 4.97 %
Rwork0.1637 96055 -
obs0.1647 101080 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.39 Å2
Refinement stepCycle: LAST / Resolution: 1.56→64.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 105 405 4442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00644255
X-RAY DIFFRACTIONf_angle_d0.8585762
X-RAY DIFFRACTIONf_chiral_restr0.0567597
X-RAY DIFFRACTIONf_plane_restr0.0083745
X-RAY DIFFRACTIONf_dihedral_angle_d15.3291586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.580.36371640.39473157X-RAY DIFFRACTION99.91
1.58-1.60.4191840.36023108X-RAY DIFFRACTION100
1.6-1.620.35671670.33783194X-RAY DIFFRACTION99.94
1.62-1.640.3411650.3043130X-RAY DIFFRACTION100
1.64-1.660.32881380.29313195X-RAY DIFFRACTION100
1.66-1.680.29941690.26293147X-RAY DIFFRACTION100
1.68-1.70.2911620.24433158X-RAY DIFFRACTION100
1.7-1.730.2651610.23773148X-RAY DIFFRACTION100
1.73-1.760.27841370.21543205X-RAY DIFFRACTION100
1.76-1.790.23071610.20623165X-RAY DIFFRACTION100
1.79-1.820.21121860.20393140X-RAY DIFFRACTION100
1.82-1.850.24581790.20943173X-RAY DIFFRACTION100
1.85-1.890.22541690.21043165X-RAY DIFFRACTION100
1.89-1.920.22261830.2043147X-RAY DIFFRACTION100
1.92-1.970.20921620.17833195X-RAY DIFFRACTION100
1.97-2.010.18791560.15573164X-RAY DIFFRACTION100
2.01-2.060.16171670.15083197X-RAY DIFFRACTION100
2.06-2.120.16231630.15273173X-RAY DIFFRACTION100
2.12-2.180.17931600.15373206X-RAY DIFFRACTION100
2.18-2.250.16721590.15223183X-RAY DIFFRACTION100
2.25-2.330.17781750.16063185X-RAY DIFFRACTION99.97
2.33-2.420.19321780.15543202X-RAY DIFFRACTION100
2.42-2.530.1811760.15843215X-RAY DIFFRACTION99.97
2.53-2.670.17291810.16443209X-RAY DIFFRACTION100
2.67-2.830.19591790.16493210X-RAY DIFFRACTION100
2.83-3.050.17671660.17043255X-RAY DIFFRACTION100
3.05-3.360.17351480.16263274X-RAY DIFFRACTION99.97
3.36-3.850.15681700.13923305X-RAY DIFFRACTION100
3.85-4.850.14061770.123319X-RAY DIFFRACTION100
4.85-64.030.16781830.14793531X-RAY DIFFRACTION99.89
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)
16.90939960881-0.25397184073-5.271087665745.93701596385-0.2535247504064.378004987290.4539247281530.1119559557680.6786616886090.315713272728-0.0382007893850.487129769776-0.84867163329-0.304981749268-0.4988782154430.2719989211440.013210244727-0.03848472075660.179361541531-0.004407095768040.32951063782351.21033860047.13680596592-23.4473948535
21.063526586220.102362046950.2470296691131.81493393109-0.2109292460041.0656517659-0.07373331135190.04060932073190.04664400138660.06162298194970.04740046619030.0502336291272-0.0636910982077-0.01619920505420.02433826225410.197827118772-0.01321203685550.008276709804940.165860824838-0.01500907471960.15183569163756.5567403126-13.2031111155-18.3086812355
37.66285610724-4.315885579174.489602453297.99053040558-5.741142540745.400818738770.0458157507828-0.495376853726-0.07595363014870.2495649491220.437024192971.27525074640.010153701533-0.612556524974-0.4837573434250.261960474448-0.1011366278410.1197546987810.395971831718-0.0697523394550.42605046810422.307249381-37.5041860487-21.1394308239
40.8755599434470.230494563515-0.2845794048451.263413585170.294057733581.92798056072-0.008673865537530.03045673662380.04045472084720.00335556196923-0.01500144459450.153128438820.0001200379986-0.1153388631190.02133878070720.158054481753-0.03130338622830.004393312984250.191841471091-0.02494782660120.20473831837337.0507456013-30.4674871085-35.4625526238
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 38 )AA21 - 381 - 18
22chain 'A' and (resid 39 through 261 )AA39 - 26119 - 241
33chain 'B' and (resid 21 through 38 )BE21 - 381 - 18
44chain 'B' and (resid 39 through 261 )BE39 - 26119 - 241

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