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- PDB-8fqu: ADC-219 in complex with boronic acid transition state inhibitor MB076 -

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Basic information

Entry
Database: PDB / ID: 8fqu
TitleADC-219 in complex with boronic acid transition state inhibitor MB076
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / BATSI / inhibitor / Acinetobacter-derived cephalosporinase / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyChem-YDB
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsPowers, R.A. / Wallar, B.J. / June, C.M. / Maurer, O.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI072219 United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Synthesis of a Novel Boronic Acid Transition State Inhibitor, MB076: A Heterocyclic Triazole Effectively Inhibits Acinetobacter -Derived Cephalosporinase Variants with an Expanded-Substrate Spectrum.
Authors: Powers, R.A. / June, C.M. / Fernando, M.C. / Fish, E.R. / Maurer, O.L. / Baumann, R.M. / Beardsley, T.J. / Taracila, M.A. / Rudin, S.D. / Hujer, K.M. / Hujer, A.M. / Santi, N. / Villamil, V. ...Authors: Powers, R.A. / June, C.M. / Fernando, M.C. / Fish, E.R. / Maurer, O.L. / Baumann, R.M. / Beardsley, T.J. / Taracila, M.A. / Rudin, S.D. / Hujer, K.M. / Hujer, A.M. / Santi, N. / Villamil, V. / Introvigne, M.L. / Prati, F. / Caselli, E. / Bonomo, R.A. / Wallar, B.J.
History
DepositionJan 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 26, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Beta-lactamase
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8048
Polymers81,7452
Non-polymers1,0596
Water13,025723
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4024
Polymers40,8731
Non-polymers5293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4024
Polymers40,8731
Non-polymers5293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.517, 172.435, 49.470
Angle α, β, γ (deg.)90.00, 111.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 40872.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ampC / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-YDB / 1-[(2R)-2-{2-[(5-amino-1,3,4-thiadiazol-2-yl)sulfanyl]acetamido}-2-boronoethyl]-1H-1,2,3-triazole-4-carboxylic acid


Mass: 373.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12BN7O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M SPG, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.49→86.22 Å / Num. obs: 81281 / % possible obs: 92 % / Redundancy: 4 % / CC1/2: 0.995 / Rpim(I) all: 0.061 / Net I/σ(I): 7.2
Reflection shellResolution: 1.49→1.65 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4063 / CC1/2: 0.595 / Rpim(I) all: 0.478

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIXv1.19refinement
Cootmodel building
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0X

4u0x


Resolution: 1.49→30.19 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 3966 4.88 %
Rwork0.1744 --
obs0.1761 81264 70.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→30.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5672 0 64 724 6460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065932
X-RAY DIFFRACTIONf_angle_d0.8858052
X-RAY DIFFRACTIONf_dihedral_angle_d13.2952214
X-RAY DIFFRACTIONf_chiral_restr0.082874
X-RAY DIFFRACTIONf_plane_restr0.0061047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.11220.24632X-RAY DIFFRACTION1
1.51-1.530.1719100.2335101X-RAY DIFFRACTION3
1.53-1.550.33740.2492247X-RAY DIFFRACTION6
1.55-1.570.309120.2388443X-RAY DIFFRACTION11
1.57-1.590.27230.2347554X-RAY DIFFRACTION14
1.59-1.610.2724450.2478760X-RAY DIFFRACTION20
1.61-1.640.2903510.24991070X-RAY DIFFRACTION27
1.64-1.660.2651530.24331342X-RAY DIFFRACTION34
1.66-1.690.29281180.2492039X-RAY DIFFRACTION52
1.69-1.720.26261340.24992641X-RAY DIFFRACTION68
1.72-1.760.27721390.2432939X-RAY DIFFRACTION74
1.76-1.790.26871960.23783567X-RAY DIFFRACTION92
1.79-1.830.25342230.21953856X-RAY DIFFRACTION98
1.83-1.870.27841970.21383818X-RAY DIFFRACTION99
1.87-1.920.23771780.20613881X-RAY DIFFRACTION98
1.92-1.970.22771830.18973914X-RAY DIFFRACTION99
1.97-2.030.22442020.1823792X-RAY DIFFRACTION99
2.03-2.10.22842120.17573871X-RAY DIFFRACTION98
2.1-2.170.21981970.17513859X-RAY DIFFRACTION98
2.17-2.260.21152120.16583856X-RAY DIFFRACTION98
2.26-2.360.21981710.17783904X-RAY DIFFRACTION99
2.36-2.490.19642080.17943852X-RAY DIFFRACTION99
2.49-2.640.21381840.17913883X-RAY DIFFRACTION98
2.64-2.850.22372070.18443849X-RAY DIFFRACTION98
2.85-3.130.22541900.17593578X-RAY DIFFRACTION91
3.13-3.580.17952090.15893794X-RAY DIFFRACTION96
3.58-4.510.16362110.12963920X-RAY DIFFRACTION99
4.51-30.190.16751950.14783936X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.75010.18060.09622.84221.72251.64890.02470.00230.0262-0.1812-0.02410.0485-0.1921-0.0659-0.00680.10890.00720.01170.08190.0240.0736-5.3557-5.406523.7732
21.37670.0192-0.29432.38940.99741.60660.05340.07820.0821-0.26210.0051-0.1037-0.3090.0091-0.05220.16740.00280.0050.09830.0020.0715-2.257-6.124814.9369
31.0542-0.86140.28641.5287-0.09171.21760.03620.17780.2772-0.1276-0.0608-0.2021-0.13190.13530.01680.0869-0.0124-0.00090.1070.03210.1651-25.735450.1983-12.4794
40.93990.3743-0.26991.0931-0.25861.627-0.0191-0.1733-0.04090.13810.0055-0.04370.09640.06550.01770.11250.0343-0.00780.1382-0.00220.0877-20.045525.922112.306
52.0151-0.66241.05930.6935-0.09121.7223-0.0385-0.28290.15020.1630.05330.038-0.0217-0.161-0.02230.12220.01040.01330.1266-0.00860.1438-28.87744.20046.2156
61.03920.04460.10061.338-0.05491.0029-0.00610.0264-0.01880.03120.0123-0.1530.08910.1697-0.00440.07010.0116-0.00310.1197-0.00120.0957-11.801433.0103-3.774
71.7717-0.90520.03351.11660.03851.18910.04630.20050.0665-0.0999-0.0263-0.0321-0.00610.0855-0.010.0801-0.0007-0.01080.11280.0050.0979-19.787939.4844-10.9956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 192 )
2X-RAY DIFFRACTION2chain 'B' and (resid 193 through 360 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2 through 62 )
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 166 )
5X-RAY DIFFRACTION5chain 'A' and (resid 167 through 228 )
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 308 )
7X-RAY DIFFRACTION7chain 'A' and (resid 309 through 359 )

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