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- PDB-9jse: Crystal Structure of PenI beta-Lactamase from Burkholderia pseudo... -

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Basic information

Entry
Database: PDB / ID: 9jse
TitleCrystal Structure of PenI beta-Lactamase from Burkholderia pseudomallei Complex with Taniborbactam
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-KJK / Beta-lactamase
Similarity search - Component
Biological speciesBurkholderia pseudomallei K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsNukaga, M. / Hoshino, T. / Mojica, M.F. / Papp-Wallace, K.M.
Funding support United States, United Kingdom, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201300019C United States
Wellcome Trust360G-Wellcome-101999/Z/13/Z United Kingdom
Department of Health & Human Services (HHS)HHSO100201900007C United States
Department of Veterans Affairs (VA, United States)BX002872 United States
CitationJournal: To Be Published
Title: Burkholderia pseudomallei PenI beta-lactamase and Variants Are Potently Inhibited by Taniborbactam
Authors: Mojica, M.F. / Hoshino, T. / Papp-Wallace, K.M. / Nukaga, M.
History
DepositionSep 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 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)28,6043
Polymers28,1231
Non-polymers4812
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint0 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.202, 52.120, 50.436
Angle α, β, γ (deg.)90.000, 92.554, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-lactamase


Mass: 28122.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The blaPenI gene minus the first 90 nucleotides, which encode its signal peptide, was cloned into the pET24a(+) plasmid using the NdeI and BamHI restriction sites
Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria)
Gene: penA, blaA, BPSS0946 / Plasmid: pET24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 (DE3) / References: UniProt: H7C785, beta-lactamase
#2: Chemical ChemComp-KJK / (3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid


Mass: 389.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28BN3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 1.92 Å3/Da / Density % sol: 36.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 80000, 0.1M ammonium sulfate, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.25→32.6 Å / Num. obs: 56254 / % possible obs: 95.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 10.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0426 / Net I/σ(I): 16.02
Reflection shellResolution: 1.25→1.295 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.3798 / Mean I/σ(I) obs: 3.12 / Num. unique obs: 5285 / CC1/2: 0.867 / % possible all: 90.56

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Processing

Software
NameVersionClassification
Aimless1.19.2_4158data scaling
PHENIX1.19.2_4158refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→32.6 Å / SU ML: 0.092 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 13.9831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1506 5199 5 %
Rwork0.1251 98772 -
obs0.1263 56253 89.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.99 Å2
Refinement stepCycle: LAST / Resolution: 1.25→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 34 259 2266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762134
X-RAY DIFFRACTIONf_angle_d1.05962916
X-RAY DIFFRACTIONf_chiral_restr0.0826331
X-RAY DIFFRACTIONf_plane_restr0.0129391
X-RAY DIFFRACTIONf_dihedral_angle_d6.8975334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.24031550.20752869X-RAY DIFFRACTION79.79
1.26-1.280.21181640.18913170X-RAY DIFFRACTION85.55
1.28-1.290.19511650.183188X-RAY DIFFRACTION87.18
1.29-1.310.20031670.16743216X-RAY DIFFRACTION88.21
1.31-1.330.1981730.16273341X-RAY DIFFRACTION87.98
1.33-1.350.17381710.16113184X-RAY DIFFRACTION88.76
1.35-1.370.20141760.16193253X-RAY DIFFRACTION88.81
1.37-1.390.18511740.15793270X-RAY DIFFRACTION88.38
1.39-1.410.20361670.15413242X-RAY DIFFRACTION88.22
1.41-1.430.18081680.1453218X-RAY DIFFRACTION88.57
1.43-1.460.18591790.13943265X-RAY DIFFRACTION87.9
1.46-1.480.17921720.13163258X-RAY DIFFRACTION87.88
1.48-1.510.16591570.13183030X-RAY DIFFRACTION82.84
1.51-1.540.14751740.1223288X-RAY DIFFRACTION89.83
1.54-1.570.14721730.11053351X-RAY DIFFRACTION91.08
1.57-1.610.15111730.1093359X-RAY DIFFRACTION91.96
1.61-1.650.1651770.10793378X-RAY DIFFRACTION91.6
1.65-1.70.1341720.10893364X-RAY DIFFRACTION91.46
1.7-1.750.13941810.11283377X-RAY DIFFRACTION91.82
1.75-1.80.14621760.11143401X-RAY DIFFRACTION91.95
1.8-1.870.13451790.11423357X-RAY DIFFRACTION91.96
1.87-1.940.11531780.11033329X-RAY DIFFRACTION91.21
1.94-2.030.1361790.10943220X-RAY DIFFRACTION88.47
2.03-2.140.141710.10563200X-RAY DIFFRACTION86.66
2.14-2.270.13061850.10323506X-RAY DIFFRACTION94.62
2.27-2.450.15531810.11463440X-RAY DIFFRACTION94.69
2.45-2.690.13991730.11293463X-RAY DIFFRACTION93.81
2.69-3.080.13671810.12653435X-RAY DIFFRACTION93.85
3.08-3.880.13281750.1163315X-RAY DIFFRACTION89.79
3.88-32.60.15971830.14673485X-RAY DIFFRACTION94.83

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