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- PDB-9hpy: Crystal structure of avibactam bound to OXA-57 -

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Basic information

Entry
Database: PDB / ID: 9hpy
TitleCrystal structure of avibactam bound to OXA-57
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / Class-D Beta-lactamase complex with a inhibitor
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsBragginton, E.C. / Hinchliffe, P. / Spencer, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure and dynamics of Burkholderia pseudomallei OXA-57, a distinctive low efficiency class D beta-lactamase with carbapenem-hydrolyzing activity
Authors: Bragginton, E.C. / Colenso, C.K. / Calvopina, K. / Hinchliffe, P. / Shaw, J.M. / Tooke, C.L. / Seng, R. / Chantratita, N. / Schofiled, C.J. / Spencer, J.
History
DepositionDec 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3012
Polymers27,0341
Non-polymers2671
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.782, 110.836, 66.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 27033.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: oxa-57 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6ZZZ2, beta-lactamase
#2: 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.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Monosaccharides (0.2 M D-Glucose, 0.2 M D-Mannose, 0.2 M D-Galactose, 0.2 M L-Fucose, 0.2 M D-Xylose, 0.2 M N-Acetyl-D-Glucosamine), 0.1 M Tris; BICINE pH 8.5, 37.5 % (v/v) ...Details: 0.12 M Monosaccharides (0.2 M D-Glucose, 0.2 M D-Mannose, 0.2 M D-Galactose, 0.2 M L-Fucose, 0.2 M D-Xylose, 0.2 M N-Acetyl-D-Glucosamine), 0.1 M Tris; BICINE pH 8.5, 37.5 % (v/v) Precipitant mix (25 % (v/v) MPD, 25 % (w/v) PEG 1000, 35 % (w/v) PEG 3350) Overnight soak in 2mM avibactam.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.912 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 2.48→55.42 Å / Num. obs: 8900 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.999 / Net I/σ(I): 9
Reflection shellResolution: 2.48→2.58 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1000 / CC1/2: 0.59

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→55.42 Å / SU ML: 0.4531 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.2358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2451 422 4.78 %
Rwork0.1925 8403 -
obs0.1953 8825 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.31 Å2
Refinement stepCycle: LAST / Resolution: 2.48→55.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 17 9 1838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791873
X-RAY DIFFRACTIONf_angle_d1.0112542
X-RAY DIFFRACTIONf_chiral_restr0.0496272
X-RAY DIFFRACTIONf_plane_restr0.0068326
X-RAY DIFFRACTIONf_dihedral_angle_d22.0442666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.840.37841420.28892730X-RAY DIFFRACTION98.86
2.84-3.580.32971210.24522785X-RAY DIFFRACTION99.18
3.58-55.420.20741590.15842888X-RAY DIFFRACTION99.8
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)
12.880464270611.465853869970.5469267122837.72358443343-0.03342054064853.537140985440.161329030243-0.1973656331480.5192929891550.325221534564-0.3389424561550.351343616202-0.1486509848820.02804281423760.1604642556650.5104411113220.0367560037810.0101165877950.3476706544040.03414012586650.53898376325125.438162155421.93926852814.54216696453
26.618562716646.141250479381.808124809687.239801146183.316420318032.667250313910.350274046247-0.1718564307630.0866846364781-0.769488899562-0.5944064648981.931975494291.32785021564-1.017894659890.1448046986420.980982253968-0.017262048368-0.2674442036510.721137007071-0.0868240805681.0485457870412.281404173111.1909967085-5.78796885898
31.80315489639-0.4093159689360.8224496606298.788924007410.7384142587443.055815863860.109453357138-0.203322155252-0.259231307941.18365749704-0.309309218978-0.2482111702810.223989810732-0.2082661192370.1879350486420.683770760306-0.02602299448660.06153986284330.4036319237810.01745741491240.48745216600726.142399940211.13054691746.62351967842
45.29526291016-0.1206269559660.4249140277937.992268030242.65952164174.104304204370.00807875464035-0.06169000290190.338594325202-0.163370035716-0.627852270070.857189778922-0.423784683536-0.360151247620.3140119366960.615713972949-0.0172143690865-0.02876772256070.401965374068-0.01439558908910.6884075482722.920375484525.77376206742.75466260501
55.19835203242-1.81899307227-0.08123675362330.719607558238-0.6566291060765.82423263787-0.424390633418-0.2155177611071.732707757970.414292243673-0.7519476489283.13627479068-0.695324625643-0.6007502121980.8824223607790.9102494186560.2731329818070.04367105429380.675563661568-0.1788152930491.3608195233115.093627407834.2490377396.44978514683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 105 )
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 169 )
4X-RAY DIFFRACTION4chain 'A' and (resid 170 through 249 )
5X-RAY DIFFRACTION5chain 'A' and (resid 250 through 266 )

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