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- PDB-5tg4: OXA-24/40 in Complex with Boronic Acid BA16 -

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Basic information

Entry
Database: PDB / ID: 5tg4
TitleOXA-24/40 in Complex with Boronic Acid BA16
ComponentsBeta-lactamase
Keywordshydrolase/hydrolase inhibitor / Inhibitor / Complex / Lactamase / OXA / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


penicillin binding / cell wall organization / beta-lactamase activity / beta-lactamase
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
D-Glyceraldehyde / BICARBONATE ION / Chem-JW1 / METHANETHIOL / beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsPowers, R.A. / Werner, J.P. / Mitchell, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2R15AI094489 United States
CitationJournal: Protein Sci. / Year: 2017
Title: Exploring the potential of boronic acids as inhibitors of OXA-24/40 beta-lactamase.
Authors: Werner, J.P. / Mitchell, J.M. / Taracila, M.A. / Bonomo, R.A. / Powers, R.A.
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 8, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Oct 4, 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
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)28,49411
Polymers27,6281
Non-polymers86610
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.347, 102.347, 85.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-305-

BCT

21A-305-

BCT

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Components

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Protein / Sugars , 2 types, 3 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: 27627.754 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
Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RLA6, beta-lactamase
#4: Sugar ChemComp-3GR / D-Glyceraldehyde / GLYCERALDEHYDE / (2R)-2,3-DIHYDROXYPROPANAL


Type: D-saccharide / Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3

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Non-polymers , 5 types, 350 molecules

#2: Chemical ChemComp-JW1 / {3-[(tert-butoxycarbonyl)amino]phenyl}boronic acid


Mass: 237.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16BNO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-MEE / METHANETHIOL


Mass: 48.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 4.05 Å3/Da / Density % sol: 69.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM TRIS-HCl, pH 8.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.44→102.35 Å / Num. obs: 82068 / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PAE

3pae


Resolution: 1.44→72.37 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.374 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.035 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13217 4037 4.9 %RANDOM
Rwork0.11211 ---
obs0.11311 77950 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.713 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.95 Å2
Refinement stepCycle: 1 / Resolution: 1.44→72.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 56 342 2322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0192222
X-RAY DIFFRACTIONr_bond_other_d0.0020.022105
X-RAY DIFFRACTIONr_angle_refined_deg2.281.9753029
X-RAY DIFFRACTIONr_angle_other_deg1.03134855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0475.052289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.6325.68495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23615388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.507158
X-RAY DIFFRACTIONr_chiral_restr0.2140.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022635
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02511
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3011.6811092
X-RAY DIFFRACTIONr_mcbond_other3.31.6791091
X-RAY DIFFRACTIONr_mcangle_it3.4962.5251400
X-RAY DIFFRACTIONr_mcangle_other3.4952.5261401
X-RAY DIFFRACTIONr_scbond_it3.7612.0641130
X-RAY DIFFRACTIONr_scbond_other3.7622.0651131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3012.9521630
X-RAY DIFFRACTIONr_long_range_B_refined4.64722.2542615
X-RAY DIFFRACTIONr_long_range_B_other4.64622.2572616
X-RAY DIFFRACTIONr_rigid_bond_restr6.61134326
X-RAY DIFFRACTIONr_sphericity_free30.9555229
X-RAY DIFFRACTIONr_sphericity_bonded12.68854399
LS refinement shellResolution: 1.441→1.479 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 295 -
Rwork0.232 5699 -
obs--99.9 %

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