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- PDB-8sqf: OXA-48 bound to inhibitor CDD-2725 -

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Basic information

Entry
Database: PDB / ID: 8sqf
TitleOXA-48 bound to inhibitor CDD-2725
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / carbapenemase / beta-lactamase / small molecule / HYDROLASE-INHIBITOR complex
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
BICARBONATE ION / Chem-WIP / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPark, S. / Judge, A. / Fan, J. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI143832 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)61,7306
Polymers60,8792
Non-polymers8514
Water4,053225
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8653
Polymers30,4401
Non-polymers4252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8653
Polymers30,4401
Non-polymers4252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.083, 123.083, 161.759
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-498-

HOH

21B-508-

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-WIP / (1M)-3'-(benzyloxy)-5-hydroxy[1,1'-biphenyl]-3,4'-dicarboxylic acid


Mass: 364.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H16O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 3.14 Å3/Da / Density % sol: 60.83 %
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: 1.00003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.3→33.8 Å / Num. obs: 56843 / % possible obs: 87.2 % / Redundancy: 16 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.9
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 16.7 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 7479 / CC1/2: 0.976 / % possible all: 80.4

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
PHENIX1.20.1_4487refinement
MOSFLM7.4.0data reduction
SCALA3.2.2data scaling
PHASER3.60.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.8 Å / SU ML: 0.2624 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0379
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2559 1647 5.1 %
Rwork0.1972 30658 -
obs0.2002 32305 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.36 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 62 225 4233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00854133
X-RAY DIFFRACTIONf_angle_d0.90575598
X-RAY DIFFRACTIONf_chiral_restr0.0526582
X-RAY DIFFRACTIONf_plane_restr0.0075720
X-RAY DIFFRACTIONf_dihedral_angle_d10.0479550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.31171320.25412265X-RAY DIFFRACTION89.44
2.37-2.450.30081260.23022463X-RAY DIFFRACTION97.4
2.45-2.530.29821290.23682530X-RAY DIFFRACTION99.7
2.53-2.630.33681560.2332521X-RAY DIFFRACTION99.81
2.63-2.750.29411220.23712558X-RAY DIFFRACTION99.89
2.75-2.90.31171120.22712570X-RAY DIFFRACTION99.85
2.9-3.080.3371420.2362571X-RAY DIFFRACTION99.93
3.08-3.320.24751520.22752543X-RAY DIFFRACTION99.85
3.32-3.650.26531300.19512591X-RAY DIFFRACTION99.78
3.65-4.180.22431450.17962596X-RAY DIFFRACTION99.64
4.18-5.260.20221590.15122627X-RAY DIFFRACTION99.93
5.26-33.80.21531420.16012823X-RAY DIFFRACTION99.97

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