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- PDB-9ue4: Serine Beta-Lactamase OXA-48 in Complex with MBL/SBL Inhibitor FB3-2 -

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Basic information

Entry
Database: PDB / ID: 9ue4
TitleSerine Beta-Lactamase OXA-48 in Complex with MBL/SBL Inhibitor FB3-2
ComponentsBeta-lactamase OXA-48
KeywordsHYDROLASE / Beta-lactamase / Serine-beta-lactamase OXA-48 / OXA-48
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
1-BUTANOL / : / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.184 Å
AuthorsLi, G.-B. / Wei, S.-Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81874291; 81502989 China
CitationJournal: To Be Published
Title: Serine Beta-Lactamase OXA-48 in Complex with Dual MBL/SBL Inhibitor FB3-2
Authors: Li, G.-B. / Wei, S.-Q.
History
DepositionApr 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: 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 OXA-48
B: Beta-lactamase OXA-48
C: Beta-lactamase OXA-48
D: Beta-lactamase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,95225
Polymers112,3914
Non-polymers2,56121
Water15,421856
1
A: Beta-lactamase OXA-48
B: Beta-lactamase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,43012
Polymers56,1962
Non-polymers1,23410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-29 kcal/mol
Surface area21090 Å2
MethodPISA
2
C: Beta-lactamase OXA-48
D: Beta-lactamase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,52213
Polymers56,1962
Non-polymers1,32611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-33 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.890, 108.871, 96.873
Angle α, β, γ (deg.)90.00, 108.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase OXA-48 / Serine-beta-lactamase OXA-48


Mass: 28097.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: OXA-48, bla OXA-48, bla_4, blaOXA-48, KPE71T_00045, SAMEA3727706_05517
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase

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Non-polymers , 5 types, 877 molecules

#2: Chemical
ChemComp-A1EO2 / 2-[[(3~{R})-5-(2-fluoranylethoxy)-1-oxidanyl-3~{H}-2,1-benzoxaborol-3-yl]methyl]prop-2-enoic acid


Mass: 280.057 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H14BFO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 856 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 5% 1-Butanol, 0.1M HEPES, pH7.5, 17% PEG8000

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jun 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 61044 / % possible obs: 99.9 % / Redundancy: 6.49 % / CC1/2: 0.9817 / Rmerge(I) obs: 0.0616 / Rpim(I) all: 0.0263 / Rrim(I) all: 0.0671 / Net I/σ(I): 32.91
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID
9.57-500.05767590.72381
6.84-9.570.047212910.99591
5.61-6.840.046216430.99821
4.86-5.610.042619510.99811
4.36-4.860.042121900.99751
3.98-4.360.044824090.9981
3.69-3.980.04726230.99621
3.45-3.690.05127990.99751
3.25-3.450.052730090.99771
3.09-3.250.060231440.99721
2.94-3.090.064333020.99531
2.82-2.940.067934930.99641
2.71-2.820.075335780.99621
2.61-2.710.079837210.99621
2.52-2.610.083439040.99151
2.44-2.520.090340300.99451
2.37-2.440.108640980.99191
2.3-2.370.108642230.99191
2.24-2.30.112743920.99111
2.18-2.240.117544850.99031

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
autoPXdata processing
autoPXdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.184→45.943 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 1998 3.28 %
Rwork0.1383 --
obs0.1402 60995 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.184→45.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 168 856 8956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148283
X-RAY DIFFRACTIONf_angle_d1.21511183
X-RAY DIFFRACTIONf_dihedral_angle_d21.7824842
X-RAY DIFFRACTIONf_chiral_restr0.0681160
X-RAY DIFFRACTIONf_plane_restr0.0071428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.184-2.23860.20671460.12684143X-RAY DIFFRACTION98
2.2386-2.29920.21841330.12574225X-RAY DIFFRACTION100
2.2992-2.36680.20211440.12574163X-RAY DIFFRACTION100
2.3668-2.44320.20641450.12924166X-RAY DIFFRACTION100
2.4432-2.53050.21051450.13354225X-RAY DIFFRACTION100
2.5305-2.63180.21131400.13334189X-RAY DIFFRACTION100
2.6318-2.75160.21061420.13894240X-RAY DIFFRACTION100
2.7516-2.89660.2051380.1444197X-RAY DIFFRACTION100
2.8966-3.07810.17741440.14734198X-RAY DIFFRACTION100
3.0781-3.31570.22881430.1594266X-RAY DIFFRACTION100
3.3157-3.64920.16461440.13964195X-RAY DIFFRACTION100
3.6492-4.1770.21171440.13124249X-RAY DIFFRACTION100
4.177-5.26140.14851440.1244236X-RAY DIFFRACTION100
5.2614-45.9430.20261460.16524305X-RAY DIFFRACTION100

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