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- PDB-4wm9: Acinetobacter baumanii OXA-24 complex with Avibactam -

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Basic information

Entry
Database: PDB / ID: 4wm9
TitleAcinetobacter baumanii OXA-24 complex with Avibactam
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / class D carbapenemase / inhibitor
Function / homology
Function and homology information


penicillin binding / beta-lactamase activity
Similarity search - Function
Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBON DIOXIDE / Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMangani, S. / Benvenuti, M. / Docquier, J.-D.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Molecular Basis of Selective Inhibition and Slow Reversibility of Avibactam against Class D Carbapenemases: A Structure-Guided Study of OXA-24 and OXA-48.
Authors: Lahiri, S.D. / Mangani, S. / Jahic, H. / Benvenuti, M. / Durand-Reville, T.F. / De Luca, F. / Ehmann, D.E. / Rossolini, G.M. / Alm, R.A. / Docquier, J.D.
History
DepositionOct 8, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4099
Polymers27,6911
Non-polymers7188
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint2 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.180, 102.180, 87.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase / Beta-lactamase OXA-33 / Betalactamase OXA24 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / ...Beta-lactamase OXA-33 / Betalactamase OXA24 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing oxacillinase / Carbapenem-hydrolyzing oxacillinase OXA-40 / Carbapenemase OXA-24 / Class D beta-lactamase OXA-40 / OXA24 B-lactamase / Oxa40


Mass: 27690.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40
Production host: Escherichia coli (E. coli) / References: UniProt: Q8RLA6

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Non-polymers , 5 types, 89 molecules

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


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Enzyme (6 mg/mL) co-crystallized with avibactam (3 mg/mL) in 0.1 M MES buffer (pH 6.0) containing 2.4 M (NH4)2SO4 as precipitant.
PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.936 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 2.4→55.82 Å / Num. obs: 17188 / % possible obs: 92.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 4 / % possible all: 94.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JC7

2jc7


Resolution: 2.4→31.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.967 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 892 5.2 %RANDOM
Rwork0.1787 16268 --
obs0.1813 16268 91.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90 Å2 / Biso mean: 28.732 Å2 / Biso min: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.4→31.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 45 81 2047
Biso mean--46.07 32.84 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191998
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.9672681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6915241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.23225.34986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.16915365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.874157
X-RAY DIFFRACTIONr_chiral_restr0.1540.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211455
X-RAY DIFFRACTIONr_mcbond_it2.552.633970
X-RAY DIFFRACTIONr_mcangle_it3.9893.9271209
X-RAY DIFFRACTIONr_scbond_it4.1733.0021027
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 68 -
Rwork0.259 1190 -
all-1258 -
obs--93.88 %

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