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- PDB-9h17: Crystal structure of OXA-405 in complex with avibactam -

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Basic information

Entry
Database: PDB / ID: 9h17
TitleCrystal structure of OXA-405 in complex with avibactam
ComponentsBeta-lactamase
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 / 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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Beta-lactamase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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)57,43316
Polymers55,7612
Non-polymers1,67214
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint2 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.302, 122.302, 160.175
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
11B-413-

HOH

21B-549-

HOH

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Components

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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 , 8 types, 432 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#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-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
#5: 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
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 3.11 Å3/Da / Density % sol: 60.39 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.46→57.13 Å / Num. obs: 122147 / % possible obs: 100 % / Redundancy: 41.8 % / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 12
Reflection shellResolution: 1.46→1.49 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6005 / CC1/2: 0.286 / Rpim(I) all: 0.818 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→57.13 Å / SU ML: 0.2025 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.8208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.196 2000 1.64 %
Rwork0.1738 119931 -
obs0.1741 121931 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.13 Å2
Refinement stepCycle: LAST / Resolution: 1.46→57.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3928 0 130 418 4476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00584204
X-RAY DIFFRACTIONf_angle_d0.80995676
X-RAY DIFFRACTIONf_chiral_restr0.0792587
X-RAY DIFFRACTIONf_plane_restr0.0077730
X-RAY DIFFRACTIONf_dihedral_angle_d15.40881565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.50.39221400.35648395X-RAY DIFFRACTION99.63
1.5-1.540.32481410.3278452X-RAY DIFFRACTION99.77
1.54-1.580.32351400.2898430X-RAY DIFFRACTION99.83
1.58-1.630.27761420.25928480X-RAY DIFFRACTION99.86
1.63-1.690.24011410.23398439X-RAY DIFFRACTION99.88
1.69-1.760.2351410.20948494X-RAY DIFFRACTION99.87
1.76-1.840.18941420.19258484X-RAY DIFFRACTION99.91
1.84-1.940.20371420.19098539X-RAY DIFFRACTION99.93
1.94-2.060.17821430.15488545X-RAY DIFFRACTION99.99
2.06-2.220.18491430.14848561X-RAY DIFFRACTION99.99
2.22-2.440.18231430.15468592X-RAY DIFFRACTION100
2.44-2.790.18621440.16138654X-RAY DIFFRACTION100
2.79-3.520.16971450.15478735X-RAY DIFFRACTION99.99
3.52-57.130.1831530.15819131X-RAY DIFFRACTION99.91
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)
12.93020604905-1.740747236422.575733135396.86848378947-3.914621375154.963517089220.1281641224860.074460188896-0.60682816462-0.362048656430.1911692476410.1705376104610.449451575077-0.296788101172-0.3187310523040.19463212291-0.08541523474910.01768676323150.276528831066-0.07415436638390.351311647297-21.290703519237.9666491324-5.59274536612
22.215188974360.9214340604121.109376895530.9841199915410.6481642524292.645878625170.0297175562290.0153554223538-0.116091908555-5.94171604743E-5-0.09942467713020.1446765599090.201316148214-0.2931161384030.08445687249520.117031797415-0.001575603215650.01410805400710.196223048333-0.03888358886590.191158954024-15.328908569146.08664528394.05426468402
31.79735232-0.6806168771080.004707773206233.236814264070.2683893348381.57582778302-0.036490684901-0.0789985292618-0.1569096392950.1002518471030.00983087502507-0.09433338415810.1094683839020.1340005348010.03297622395550.145642178179-0.0128665887355-0.006923278630710.2303374581490.008638400893560.1868096166243.3274800923946.520022271219.3834708773
49.20818883881-2.398168455576.806392716353.11994007825-1.968886141825.05139108126-0.10874199059-0.151192496850.09827030827150.1548578221220.1184453669340.219190990726-0.6073621633430.0176789160557-0.02835541980270.1831929494680.002005900753450.03417801368520.197939111957-0.02821403647860.179610947117-12.411432633159.822541214619.8121688049
51.962144035370.499636965151-0.6446096030441.116773210290.2252239091292.002163784090.0200425277762-0.01184977880880.01410861376360.0217205976433-0.03201753074540.12253479255-0.0252801700665-0.14187495771-0.002926496820360.123894676217-0.00498210253295-0.003957712362960.17755533874-0.0114524968020.152497378236-10.877769535853.701110791710.7601717641
65.79881852440.954615853071-3.235681229773.32727955068-1.541642893947.30599750042-0.188992122970.190647000168-0.414514330534-0.1310255000130.0757797698342-0.001133182130340.380660912935-0.2630361802370.1562504239370.112161548846-0.0373639169098-0.007418270963760.145944777704-0.02682132924280.180127479358-2.9230508829842.71968212081.8864459612
76.028971044532.54442619699-1.778965485194.21944452026-1.846018632135.207506539650.000427447837928-0.0788662705746-0.278274056293-0.0023256969041-0.1024534612160.03856196754180.266785749021-0.09792179420110.06284425122430.115422842281-0.018154938007-0.001442987829280.141932862808-0.05594863673080.152825303558-10.76884330142.77215118390.912694289461
86.88072782104-0.2563466267972.471919207095.143442737320.4845126797117.10848628670.150488626243-0.0514809469621-0.7813753069220.110247533448-0.0234437864006-0.2056553694910.70899570661-0.0802742231223-0.08774159282460.1941546056-0.0330298239210.007050817788830.161589003987-0.08533892123760.37477595027-9.6331848578934.4136885796-1.47955245321
93.85258016459-0.07592489319811.722340029016.627552003534.438854859416.905151866450.1507076000880.323113404021-0.5237596497690.03681570442930.117749800977-0.1949028389440.4146743905290.586611406221-0.2871688549140.1712203537990.05861863822560.02483702823040.214751096016-0.001187675335170.29991121689631.869741665740.6707430795-3.26847028275
102.05284648895-0.8850978587940.6473918216171.39160340393-0.668913865130.8168223643080.05576220104320.0328715278936-0.102013684149-0.0276124008325-0.0664383834409-0.08140756584270.06239362275310.1090114215580.02937533728590.1526806545060.003588186893250.009928285269320.201955374871-0.005002577148040.1608469402424.7223936952.4345220307-4.92820009087
112.114272875381.201958752460.8518027737064.867551655644.16207404037.889885014180.04309164145770.2422194876380.0331128026014-0.4348533962-0.04285605911350.179538215036-0.170396817373-0.3532434178320.0386267378050.1771684543310.0414607650976-0.03441663965450.2154007826840.01764979166020.1862245184092.8702363487162.3907928667-17.7838189482
125.96705694154-3.22270745689-3.855368367816.8743781161-1.89084780386.22267590614-0.02144302645770.112792148725-0.179425255121-0.319251647828-0.0377919744940.09486533492210.113925330427-0.2636337694260.08594521269740.119385222235-0.0176993663234-0.02000868433870.172254317587-0.03588779313780.1577026213664.8911780357755.0849614038-16.892065234
138.26250749013.67388926086.996512109164.397287845973.695191248547.63483192824-0.190476446243-0.002831785827080.231423823546-0.2193652538770.03350663811490.0503827725088-0.404000892611-0.02779429681910.1823726248730.1665249842180.02408025682810.04922023322220.1616772732230.0003178944105960.1347053788314.646441678669.4560302544-13.0991402522
141.469900652380.12734104204-0.3011829088110.889775489605-0.5807647980251.195416364550.0918904846832-0.06808859805360.06781382503360.0175350166407-0.113588087781-0.0451519523445-0.09166028946640.1627570263750.02672118998820.173033270107-0.00216866582802-0.004255989031390.203926152554-0.005579779795550.16205333648119.21331517562.0460036483-5.53763325869
154.30464513629-0.1560605188160.1958749101031.93942054921-0.08481121671332.289664640340.03471645304060.18305887927-0.184726715551-0.106690175746-0.0290816652485-0.04015482017920.1515222126640.1144049734420.03548748047160.1067200969070.0140664713680.006919331248740.120073884913-0.01818544283340.13295281701417.350447783947.3296614913-5.39918114742
166.336967915050.144673790649-0.2948840417615.97069379491-0.5391221560028.824405223360.1518976852350.517374204346-0.499935737972-0.509945303557-0.1167425543280.3122793324230.4043737610110.098868235677-0.04379839039190.1899643878010.0328886829537-0.001150781620150.177858396209-0.07545497388280.25143200549120.493106583439.5654768697-9.21287144449
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 82 )AA39 - 8219 - 62
33chain 'A' and (resid 83 through 130 )AA83 - 13063 - 110
44chain 'A' and (resid 131 through 141 )AA131 - 141111 - 121
55chain 'A' and (resid 142 through 194 )AA142 - 194122 - 174
66chain 'A' and (resid 195 through 213 )AA195 - 213175 - 193
77chain 'A' and (resid 214 through 237 )AA214 - 237194 - 217
88chain 'A' and (resid 238 through 261 )AA238 - 261218 - 241
99chain 'B' and (resid 21 through 38 )BG21 - 381 - 18
1010chain 'B' and (resid 39 through 82 )BG39 - 8219 - 62
1111chain 'B' and (resid 83 through 102 )BG83 - 10263 - 82
1212chain 'B' and (resid 103 through 119 )BG103 - 11983 - 99
1313chain 'B' and (resid 120 through 141 )BG120 - 141100 - 121
1414chain 'B' and (resid 142 through 194 )BG142 - 194122 - 174
1515chain 'B' and (resid 195 through 237 )BG195 - 237175 - 217
1616chain 'B' and (resid 238 through 261 )BG238 - 261218 - 241

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