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- PDB-8sqg: OXA-48 bound to inhibitor CDD-2801 -

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Basic information

Entry
Database: PDB / ID: 8sqg
TitleOXA-48 bound to inhibitor CDD-2801
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / carbapenemase / beta-lactamase / serine protease / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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
BICARBONATE ION / Chem-X6Q / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsPark, S. / Judge, A. / Fan, J. / Sankaran, B. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Exploiting the Carboxylate-Binding Pocket of beta-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library.
Authors: Park, S. / Fan, J. / Chamakuri, S. / Palaniappan, M. / Sharma, K. / Qin, X. / Wang, J. / Tan, Z. / Judge, A. / Hu, L. / Sankaran, B. / Li, F. / Prasad, B.V.V. / Matzuk, M.M. / Palzkill, T.
History
DepositionMay 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Beta-lactamase
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8726
Polymers60,8792
Non-polymers9934
Water4,738263
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9363
Polymers30,4401
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9363
Polymers30,4401
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.929, 121.929, 160.522
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11B-507-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 30439.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: OXA-48 Beta-lactamase / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0
#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CHO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-X6Q / (1M)-3'-(benzyloxy)-5-[2-(methylamino)-2-oxoethoxy][1,1'-biphenyl]-3,4'-dicarboxylic acid


Mass: 435.426 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H21NO7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.06 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% (v/v) PEG 550 MME, 0.1 M TRIS-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 16, 2022
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.03→33.52 Å / Num. obs: 46045 / % possible obs: 99.88 % / Redundancy: 22.7 % / Biso Wilson estimate: 27.02 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.08
Reflection shellResolution: 2.03→2.103 Å / Mean I/σ(I) obs: 3.35 / Num. unique obs: 4529 / CC1/2: 0.914

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Processing

Software
NameVersionClassification
REFMAC5.0.32refinement
PHENIX1.20.1_4487refinement
MOSFLM7.4.0data reduction
SCALA3.2.2data scaling
PHASER3.60.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→33.52 Å / SU ML: 0.2269 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3515
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 2426 5.27 %
Rwork0.1914 43587 -
obs0.1935 46010 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.73 Å2
Refinement stepCycle: LAST / Resolution: 2.03→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3927 0 72 263 4262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764141
X-RAY DIFFRACTIONf_angle_d0.85515620
X-RAY DIFFRACTIONf_chiral_restr0.0554586
X-RAY DIFFRACTIONf_plane_restr0.0061726
X-RAY DIFFRACTIONf_dihedral_angle_d14.8696562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.070.30331510.25632518X-RAY DIFFRACTION99.93
2.07-2.120.27971330.23652495X-RAY DIFFRACTION99.92
2.12-2.170.25631330.22592536X-RAY DIFFRACTION100
2.17-2.220.26961620.22232502X-RAY DIFFRACTION99.96
2.22-2.280.27621540.22252485X-RAY DIFFRACTION99.81
2.28-2.350.27191380.21342553X-RAY DIFFRACTION99.96
2.35-2.420.25411420.20582501X-RAY DIFFRACTION99.32
2.42-2.510.23791510.20172518X-RAY DIFFRACTION100
2.51-2.610.28671160.20932566X-RAY DIFFRACTION99.96
2.61-2.730.28331390.20512557X-RAY DIFFRACTION99.96
2.73-2.870.24861430.20632545X-RAY DIFFRACTION99.96
2.87-3.050.28311410.212586X-RAY DIFFRACTION100
3.05-3.290.25071380.20282563X-RAY DIFFRACTION100
3.29-3.620.20721510.1822570X-RAY DIFFRACTION100
3.62-4.140.18991270.16652638X-RAY DIFFRACTION100
4.14-5.210.16121510.15412639X-RAY DIFFRACTION100
5.21-33.520.19471560.17822815X-RAY DIFFRACTION99.97

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