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- PDB-6q5b: OXA-48_P68A-AVI. Evolutionary trade-offs of OXA-48 mediated cefta... -

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Basic information

Entry
Database: PDB / ID: 6q5b
TitleOXA-48_P68A-AVI. Evolutionary trade-offs of OXA-48 mediated ceftazidime-avibactam resistance
Components(Beta-lactamase) x 2
KeywordsANTIBIOTIC / OXA-48 / ceftazidime / avibactam / resistance development / evolution / Escherichia coli / Klebsiella pneumoniae / carbapenemase / carbapenem
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBON DIOXIDE / Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsFrohlich, C. / Sorum, V. / Thomassen, A.M. / Johnsen, P.J. / Leiros, H.K.S. / Samuelsen, O.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of NorwayA32689 Norway
CitationJournal: Msphere / Year: 2019
Title: OXA-48-Mediated Ceftazidime-Avibactam Resistance Is Associated with Evolutionary Trade-Offs.
Authors: Frohlich, C. / Sorum, V. / Thomassen, A.M. / Johnsen, P.J. / Leiros, H.S. / Samuelsen, O.
History
DepositionDec 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 8, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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)122,96415
Polymers121,5694
Non-polymers1,39511
Water12,592699
1
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4698
Polymers60,7842
Non-polymers6856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-19 kcal/mol
Surface area20310 Å2
MethodPISA
2
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4947
Polymers60,7842
Non-polymers7105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-26 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.115, 105.802, 125.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Beta-lactamase /


Mass: 30370.686 Da / Num. of mol.: 2 / Mutation: P68A
Source method: isolated from a genetically manipulated source
Details: A P68A mutatnt / Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_2, bla_4, blaOXA-48, KPE71T_00045, SAMEA3673128_05462, SAMEA3727643_05844, SAMEA3729690_05506
Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Protein Beta-lactamase /


Mass: 30413.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_2, bla_4, blaOXA-48, KPE71T_00045, SAMEA3673128_05462, SAMEA3727643_05844, SAMEA3729690_05506
Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase

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Non-polymers , 5 types, 710 molecules

#3: Chemical
ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form / Avibactam


Mass: 267.260 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic, inhibitor*YM
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 to 30 % polyethylene glycol monomethyl ether 5,000 and 0.1 M bis-tris propane buffer pH 6.5 to 7.5
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.22→25 Å / Num. obs: 58434 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 2.22 % / CC1/2: 0.994 / Rmerge(I) obs: 0.196 / Net I/σ(I): 6.8
Reflection shellResolution: 2.22→2.28 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5QB4

5qb4


Resolution: 2.22→24.831 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 2188 3.76 %
Rwork0.204 --
obs0.2062 58236 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→24.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7758 0 83 699 8540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128053
X-RAY DIFFRACTIONf_angle_d1.1810889
X-RAY DIFFRACTIONf_dihedral_angle_d21.5514725
X-RAY DIFFRACTIONf_chiral_restr0.061144
X-RAY DIFFRACTIONf_plane_restr0.0071396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.26830.35571100.26793476X-RAY DIFFRACTION100
2.2683-2.3210.32471590.27323445X-RAY DIFFRACTION100
2.321-2.3790.32131450.26083428X-RAY DIFFRACTION100
2.379-2.44330.29391240.25263473X-RAY DIFFRACTION100
2.4433-2.51510.32291260.24393499X-RAY DIFFRACTION100
2.5151-2.59620.32751230.24183470X-RAY DIFFRACTION100
2.5962-2.68890.3021460.23163447X-RAY DIFFRACTION100
2.6889-2.79640.28591510.21453475X-RAY DIFFRACTION100
2.7964-2.92350.29551420.21663482X-RAY DIFFRACTION100
2.9235-3.07730.26111280.21213491X-RAY DIFFRACTION100
3.0773-3.26980.27581350.20713538X-RAY DIFFRACTION100
3.2698-3.52160.24941490.18843474X-RAY DIFFRACTION99
3.5216-3.87480.24311340.16593525X-RAY DIFFRACTION100
3.8748-4.43270.20921490.1573558X-RAY DIFFRACTION100
4.4327-5.57430.18631410.16013556X-RAY DIFFRACTION99
5.5743-24.83260.27851260.2193711X-RAY DIFFRACTION99

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