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- PDB-9ueh: Serine Beta-Lactamase OXA-48 in Complex with MBL/SBL Inhibitor FB1-10 -

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Basic information

Entry
Database: PDB / ID: 9ueh
TitleSerine Beta-Lactamase OXA-48 in Complex with MBL/SBL Inhibitor FB1-10
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 / beta-lactamase activity / 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: 1.756 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 FB1-10
Authors: Li, G.-B. / Wei, S.-Q.
History
DepositionApr 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 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)113,92411
Polymers112,3914
Non-polymers1,5337
Water10,773598
1
A: Beta-lactamase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4212
Polymers28,0981
Non-polymers3231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4953
Polymers28,0981
Non-polymers3972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5133
Polymers28,0981
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4953
Polymers28,0981
Non-polymers3972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.513, 105.474, 94.144
Angle α, β, γ (deg.)90.00, 108.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical
ChemComp-A1EO1 / 7-[3-(2-fluoranylethylamino)cyclobutyl]oxy-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid


Mass: 323.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H19BFNO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 5% 1-Butanol, 0.1M HEPES, pH7.5, 15-17% 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: Mar 24, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.756→50 Å / Num. obs: 106244 / % possible obs: 98.5 % / Redundancy: 6.44 % / CC1/2: 0.5819 / Rmerge(I) obs: 0.5333 / Rpim(I) all: 0.2331 / Rrim(I) all: 0.5837 / Net I/σ(I): 9.38
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID
7.76-500.056612630.99661
5.52-7.760.081422480.99441
4.52-5.520.070527990.99621
3.92-4.520.077933490.99581
3.51-3.920.094138670.99321
3.2-3.510.117941950.98991
2.97-3.20.149444990.98091
2.77-2.970.401648780.94551
2.62-2.770.348152360.91891
2.48-2.620.280855360.95251
2.37-2.480.303757000.92581
2.27-2.370.389860440.89251
2.18-2.270.511562800.83391
2.1-2.180.522565800.8341
2.03-2.10.592367960.79271
1.96-2.031.299168840.12871
1.9-1.960.947572270.52241
1.85-1.91.382474380.40251
1.8-1.851.380776320.34491
1.76-1.83.17677930.00551

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
SCALEPACKdata scaling
autoPXdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DML

7dml


Resolution: 1.756→49.247 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 1990 1.88 %
Rwork0.1972 --
obs0.198 105884 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.756→49.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7896 0 108 598 8602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128209
X-RAY DIFFRACTIONf_angle_d1.14311103
X-RAY DIFFRACTIONf_dihedral_angle_d21.5924786
X-RAY DIFFRACTIONf_chiral_restr0.0611160
X-RAY DIFFRACTIONf_plane_restr0.0071416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7563-1.80020.41921370.36327165X-RAY DIFFRACTION95
1.8002-1.84890.35691420.3197416X-RAY DIFFRACTION98
1.8489-1.90330.33061440.30047416X-RAY DIFFRACTION98
1.9033-1.96470.36561400.2747445X-RAY DIFFRACTION98
1.9647-2.03490.29471410.24927266X-RAY DIFFRACTION97
2.0349-2.11640.25561420.21777492X-RAY DIFFRACTION99
2.1164-2.21270.25381430.20547462X-RAY DIFFRACTION99
2.2127-2.32940.24931440.20647470X-RAY DIFFRACTION99
2.3294-2.47530.24911420.19327381X-RAY DIFFRACTION98
2.4753-2.66640.23061460.18647497X-RAY DIFFRACTION99
2.6664-2.93470.28541380.21237424X-RAY DIFFRACTION98
2.9347-3.35930.20471460.17687409X-RAY DIFFRACTION98
3.3593-4.2320.19571410.15357523X-RAY DIFFRACTION99
4.232-49.2470.1751440.15927528X-RAY DIFFRACTION98

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