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- PDB-7khq: Crystal structure of OXA-48 K73A in complex with meropenem -

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Basic information

Entry
Database: PDB / ID: 7khq
TitleCrystal structure of OXA-48 K73A in complex with meropenem
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / carbapenemase / beta-lactamase inhibitor / complex / oxacillinase / HYDROLASE-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 / 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
Chem-MER / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPalzkill, T. / Hu, L. / Sankaran, B. / Prasad, B.V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Mechanistic Basis of OXA-48-like beta-Lactamases' Hydrolysis of Carbapenems.
Authors: Stojanoski, V. / Hu, L. / Sankaran, B. / Wang, F. / Tao, P. / Prasad, B.V.V. / Palzkill, T.
History
DepositionOct 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,43110
Polymers56,3882
Non-polymers1,0448
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-92 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.285, 105.487, 125.665
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-492-

HOH

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Components

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


Mass: 28193.947 Da / Num. of mol.: 2 / Mutation: K73A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_2, bla_3, blaOXA-48, B6R99_29845, G5637_27540, GJJ01_28680, KPE71T_00045, SAMEA3649466_05396, SAMEA3673128_05462, SAMEA3729780_05587
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200 mM lithium acetate dihydrate and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2014
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 2→34.24 Å / Num. obs: 40232 / % possible obs: 99.1 % / Redundancy: 8.3 % / Biso Wilson estimate: 25.55 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.02
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1925 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.19rc3_4028refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2→34.24 Å / SU ML: 0.2273 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2362 1989 4.95 %
Rwork0.2073 38153 -
obs0.2087 40142 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.17 Å2
Refinement stepCycle: LAST / Resolution: 2→34.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 58 281 4283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00454096
X-RAY DIFFRACTIONf_angle_d0.61555552
X-RAY DIFFRACTIONf_chiral_restr0.0446590
X-RAY DIFFRACTIONf_plane_restr0.004720
X-RAY DIFFRACTIONf_dihedral_angle_d5.5122556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.30361540.26072643X-RAY DIFFRACTION98.52
2.05-2.110.29651420.24892725X-RAY DIFFRACTION99.83
2.11-2.170.28081200.23942695X-RAY DIFFRACTION99.4
2.17-2.240.24971280.23522712X-RAY DIFFRACTION99.44
2.24-2.320.26741430.22892704X-RAY DIFFRACTION99.48
2.32-2.410.28061560.23282684X-RAY DIFFRACTION99.68
2.41-2.520.25881430.22312726X-RAY DIFFRACTION99.45
2.52-2.650.27361410.22932730X-RAY DIFFRACTION99.34
2.65-2.820.28611390.22412696X-RAY DIFFRACTION99.09
2.82-3.040.25591410.21612727X-RAY DIFFRACTION98.46
3.04-3.340.22731390.20532717X-RAY DIFFRACTION98.14
3.34-3.830.21041520.18282723X-RAY DIFFRACTION97.92
3.83-4.820.20151370.17232714X-RAY DIFFRACTION96.06
4.82-34.240.19221540.19362957X-RAY DIFFRACTION99.87

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