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- PDB-7kh9: Crystal structure of OXA-48 K73A in complex with imipenem -

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Basic information

Entry
Database: PDB / ID: 7kh9
TitleCrystal structure of OXA-48 K73A in complex with imipenem
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-IM2 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.29 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 20, 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
B: Beta-lactamase
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1328
Polymers56,3882
Non-polymers7456
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-54 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.690, 104.750, 125.070
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

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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-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3O4S / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris-HCl pH 8.5, 15% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.29→26.9 Å / Num. obs: 53411 / % possible obs: 99 % / Redundancy: 2 % / Biso Wilson estimate: 27.09 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.0506 / Net I/σ(I): 10.73
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 2 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.15 / Num. unique obs: 5218 / CC1/2: 0.843 / % possible all: 99

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Processing

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

3hbr


Resolution: 2.29→26.87 Å / SU ML: 0.2567 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 22.6012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2271 2618 5.2 %
Rwork0.1837 47734 -
obs0.1859 50352 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.38 Å2
Refinement stepCycle: LAST / Resolution: 2.29→26.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3933 0 44 341 4318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00294071
X-RAY DIFFRACTIONf_angle_d0.76855514
X-RAY DIFFRACTIONf_chiral_restr0.0572584
X-RAY DIFFRACTIONf_plane_restr0.0055717
X-RAY DIFFRACTIONf_dihedral_angle_d4.9418548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.330.31021390.25042519X-RAY DIFFRACTION97.94
2.33-2.380.26241460.24092502X-RAY DIFFRACTION98.4
2.38-2.420.24721250.22942490X-RAY DIFFRACTION98.87
2.42-2.480.30041530.23332502X-RAY DIFFRACTION97.83
2.48-2.540.25821180.21522501X-RAY DIFFRACTION99.28
2.54-2.60.29441220.21372576X-RAY DIFFRACTION98.79
2.6-2.670.29211370.21662463X-RAY DIFFRACTION98.26
2.67-2.750.281530.21542517X-RAY DIFFRACTION98.74
2.75-2.840.30241670.21362452X-RAY DIFFRACTION97.91
2.84-2.940.27721290.21132524X-RAY DIFFRACTION98.37
2.94-3.050.30621270.21352524X-RAY DIFFRACTION98.37
3.05-3.190.21621390.21752509X-RAY DIFFRACTION97.86
3.19-3.360.21981300.18332503X-RAY DIFFRACTION98.87
3.36-3.570.21191660.17722490X-RAY DIFFRACTION98.59
3.57-3.850.20861180.16042509X-RAY DIFFRACTION98.61
3.85-4.230.18081500.15212513X-RAY DIFFRACTION98.78
4.23-4.840.16741230.13882542X-RAY DIFFRACTION99.4
4.84-6.090.17491600.15252519X-RAY DIFFRACTION99.85
6.09-26.870.18451160.14752579X-RAY DIFFRACTION99.78

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