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- PDB-5tg5: OXA-24/40 in Complex with Boronic Acid BA8 -

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Basic information

Entry
Database: PDB / ID: 5tg5
TitleOXA-24/40 in Complex with Boronic Acid BA8
ComponentsBeta-lactamase
Keywordshydrolase/hydrolase inhibitor / Inhibitor / Complex / Lactamase / OXA / hydrolase-hydrolase inhibitor complex
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
BICARBONATE ION / {4-[(azetidin-1-yl)sulfonyl]phenyl}boronic acid / METHANETHIOL / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.4Oct 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 1.5Nov 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)28,4818
Polymers27,6721
Non-polymers8097
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.974, 102.974, 86.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 27671.764 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

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Non-polymers , 5 types, 179 molecules

#2: Chemical ChemComp-JW8 / {4-[(azetidin-1-yl)sulfonyl]phenyl}boronic acid


Mass: 241.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12BNO4S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 61.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MEE / METHANETHIOL / Methanethiol


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


Mass: 18.015 Da / Num. of mol.: 172 / 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: 4.15 Å3/Da / Density % sol: 70.39 %
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-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.75→102.97 Å / Num. obs: 45159 / % possible obs: 95 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 12

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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: 1.75→72.81 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.922 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20735 2308 5.1 %RANDOM
Rwork0.17777 ---
obs0.1792 42819 94.92 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 32.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å20 Å2
2---1.94 Å20 Å2
3---3.88 Å2
Refinement stepCycle: 1 / Resolution: 1.75→72.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 51 172 2148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192057
X-RAY DIFFRACTIONr_bond_other_d0.0010.021968
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9762788
X-RAY DIFFRACTIONr_angle_other_deg0.96534526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1185.059255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90425.34188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49615362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.002158
X-RAY DIFFRACTIONr_chiral_restr0.1540.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02468
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_it2.8222.941998
X-RAY DIFFRACTIONr_mcbond_other2.7882.938997
X-RAY DIFFRACTIONr_mcangle_it4.14.4021252
X-RAY DIFFRACTIONr_mcangle_other4.1084.4041253
X-RAY DIFFRACTIONr_scbond_it4.2753.4921059
X-RAY DIFFRACTIONr_scbond_other4.2733.4981060
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6925.0151531
X-RAY DIFFRACTIONr_long_range_B_refined8.14635.2512319
X-RAY DIFFRACTIONr_long_range_B_other8.06534.7992277
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 170 -
Rwork0.324 3250 -
obs--99.25 %

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