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- PDB-5tg6: OXA-24/40 in Complex with Boronic Acid BA4 -

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Basic information

Entry
Database: PDB / ID: 5tg6
TitleOXA-24/40 in Complex with Boronic Acid BA4
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
BICARBONATE ION / Chem-J4W / beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / 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)28,1765
Polymers27,6741
Non-polymers5024
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.418, 102.418, 85.049
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-593-

HOH

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Components

#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: 27673.846 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 BL21(DE3) (bacteria) / References: UniProt: Q8RLA6
#2: Chemical ChemComp-J4W / tert-butyl (1-hydroxy-1,3-dihydro-2,1-benzoxaborol-6-yl)carbamate


Mass: 249.071 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16BNO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 4.17 Å3/Da / Density % sol: 70.54 %
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: 1.78→86.68 Å / Num. obs: 41363 / % possible obs: 93.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.4

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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: 1.78→72.42 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.911 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19244 2104 5.1 %RANDOM
Rwork0.16745 ---
obs0.16874 39199 93.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.738 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20 Å2
2---1.13 Å20 Å2
3---2.25 Å2
Refinement stepCycle: 1 / Resolution: 1.78→72.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 32 199 2150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192054
X-RAY DIFFRACTIONr_bond_other_d0.0020.021964
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9642789
X-RAY DIFFRACTIONr_angle_other_deg0.94234516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4765258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41125.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98815362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.647158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022338
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02469
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_it2.0632.4961014
X-RAY DIFFRACTIONr_mcbond_other2.0482.4941013
X-RAY DIFFRACTIONr_mcangle_it3.0963.7421278
X-RAY DIFFRACTIONr_mcangle_other3.0973.7431279
X-RAY DIFFRACTIONr_scbond_it3.2292.8911040
X-RAY DIFFRACTIONr_scbond_other3.2082.8531030
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0074.1181497
X-RAY DIFFRACTIONr_long_range_B_refined6.29430.142365
X-RAY DIFFRACTIONr_long_range_B_other6.13929.5782313
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.776→1.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 157 -
Rwork0.253 3043 -
obs--99.81 %

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