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- PDB-9ksa: Serine Beta-Lactamase OXA-48 in Complex with MBL/SBL Inhibitor CB1 -

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Basic information

Entry
Database: PDB / ID: 9ksa
TitleSerine Beta-Lactamase OXA-48 in Complex with MBL/SBL Inhibitor CB1
ComponentsBeta-lactamase
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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.178 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: OXA-48 carbapenemase in complex with 7-((1H-pyrazol-1-yl)methyl)-2-hydroxy-2,3-dihydrobenzo[e][1,4,2]dioxaborinine-8-carboxylic acid
Authors: Li, G.-B. / Wei, S.-Q.
History
DepositionNov 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 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
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4878
Polymers112,3914
Non-polymers1,0964
Water6,846380
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3722
Polymers28,0981
Non-polymers2741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3722
Polymers28,0981
Non-polymers2741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3722
Polymers28,0981
Non-polymers2741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3722
Polymers28,0981
Non-polymers2741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.596, 58.701, 105.855
Angle α, β, γ (deg.)90.00, 104.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28097.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, PHDFNENF_00011 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A866WQ05, beta-lactamase
#2: Chemical
ChemComp-A1EG0 / 2-oxidanyl-7-(pyrazol-1-ylmethyl)-3~{H}-1,4,2-benzodioxaborinine-8-carboxylic acid


Mass: 274.037 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H11BN2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 5% 1-Butanol, 0.1M HEPES, pH7.5, 15% 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: 2.178→50 Å / Num. obs: 65292 / % possible obs: 100 % / Redundancy: 6.36 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 18.07
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rsym valueDiffraction-ID
9.56-500.06798410.99250.07511
6.83-9.560.070687290.99640.07721
2.18-2.240.427647160.88580.47021

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Processing

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

7dml


Resolution: 2.178→47.9943 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 2000 3.07 %
Rwork0.2051 --
obs0.2068 65233 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.178→47.9943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7918 0 80 380 8378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158202
X-RAY DIFFRACTIONf_angle_d1.2511108
X-RAY DIFFRACTIONf_dihedral_angle_d22.3054788
X-RAY DIFFRACTIONf_chiral_restr0.0661154
X-RAY DIFFRACTIONf_plane_restr0.0071428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1783-2.23280.31221360.28324344X-RAY DIFFRACTION97
2.2328-2.29310.32351480.25194493X-RAY DIFFRACTION100
2.2931-2.36060.27541430.24194500X-RAY DIFFRACTION100
2.3606-2.43680.27811450.2464492X-RAY DIFFRACTION100
2.4368-2.52380.31471380.23414508X-RAY DIFFRACTION100
2.5238-2.62490.30721390.23354472X-RAY DIFFRACTION100
2.6249-2.74430.28561470.23694500X-RAY DIFFRACTION100
2.7443-2.88890.26851420.23464529X-RAY DIFFRACTION100
2.8889-3.06990.30351470.23234509X-RAY DIFFRACTION100
3.0699-3.30680.31221410.23384512X-RAY DIFFRACTION100
3.3068-3.63930.28841410.20614557X-RAY DIFFRACTION100
3.6393-4.16540.24951440.18064561X-RAY DIFFRACTION100
4.1654-5.24580.19911460.1554580X-RAY DIFFRACTION100
5.2458-38.40680.19911430.17184676X-RAY DIFFRACTION100

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