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- PDB-4wmc: OXA-48 covalent complex with Avibactam inhibitor -

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Basic information

Entry
Database: PDB / ID: 4wmc
TitleOXA-48 covalent complex with Avibactam inhibitor
Components(Beta-lactamase) x 2
KeywordsHYDROLASE / OXA-48 / Class D carbapenemase / Avibactam / inhibitor
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 / 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 OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 2.0Aug 25, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.details / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
E: Beta-lactamase
F: Beta-lactamase
G: Beta-lactamase
H: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,79419
Polymers224,5248
Non-polymers2,27011
Water4,612256
1
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6885
Polymers56,1102
Non-polymers5793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-lactamase
F: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7326
Polymers56,1102
Non-polymers6234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Beta-lactamase
E: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7304
Polymers56,1962
Non-polymers5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Beta-lactamase
H: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6444
Polymers56,1102
Non-polymers5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.886, 165.465, 108.524
Angle α, β, γ (deg.)90.000, 90.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase


Mass: 28054.768 Da / Num. of mol.: 6 / Fragment: UNP residues 24-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Protein Beta-lactamase


Mass: 28097.770 Da / Num. of mol.: 2 / Fragment: UNP residues 24-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#3: 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.: 8 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic*YM
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 10% PEG8000, 5-8% 1-butanol, 10 mg/mL OXA-48, and 3 mg/mL avibactam

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9834 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9834 Å / Relative weight: 1
ReflectionResolution: 2.3→65.8 Å / Num. obs: 99733 / % possible obs: 93.4 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.9 / Num. unique all: 12691 / % possible all: 88

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.3→63.88 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.862 / SU B: 8.172 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.418 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 4546 5 %RANDOM
Rwork0.2105 85927 --
obs0.2136 85927 90.71 %-
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: 28.71 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.01 Å2
2---0 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.3→63.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15281 0 145 256 15682
Biso mean--37.47 20.72 -
Num. residues----1873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01915807
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.92521398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05851852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70524.461807
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.928152706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5441590
X-RAY DIFFRACTIONr_chiral_restr0.1270.22272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212018
X-RAY DIFFRACTIONr_mcbond_it2.1572.817471
X-RAY DIFFRACTIONr_mcangle_it3.3894.1979302
X-RAY DIFFRACTIONr_scbond_it2.3812.9468336
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 312 -
Rwork0.235 5821 -
all-6133 -
obs--83.06 %

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