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- PDB-8fqw: ADC-30 in complex with boronic acid transition state inhibitor MB076 -

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Basic information

Entry
Database: PDB / ID: 8fqw
TitleADC-30 in complex with boronic acid transition state inhibitor MB076
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / BATSI / Acinetobacter-derived Cephalosporinase / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
PHOSPHATE ION / Chem-YDB / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsPowers, R.A. / Wallar, B.J. / June, C.M. / Ruiz, V.J.
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 20, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,3557
Polymers81,3412
Non-polymers1,0145
Water8,899494
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3125
Polymers40,6701
Non-polymers6414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0442
Polymers40,6701
Non-polymers3731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.435, 83.440, 179.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 40670.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaADC-30, AB237_1031 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E1PRG7, beta-lactamase
#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.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 1.91 Å3/Da / Density % sol: 35.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ADC-30 (3.5 mg/mL) in 25% w/v polyethylene glycol (PEG) 1500, 0.1 M succinate/ phosphate/ glycine

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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 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.587→89.905 Å / Num. obs: 54143 / % possible obs: 86.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Net I/σ(I): 13.1
Reflection shellResolution: 1.587→1.779 Å / Redundancy: 7 % / Rmerge(I) obs: 1.129 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2798 / CC1/2: 0.652 / Rpim(I) all: 0.454 / % possible all: 57.1

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Processing

Software
NameVersionClassification
PHENIXv1.19.2refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0X

4u0x


Resolution: 1.59→44.95 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 2715 5.02 %0.5
Rwork0.1883 ---
obs0.1904 54137 63.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5460 0 62 494 6016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055734
X-RAY DIFFRACTIONf_angle_d0.6967828
X-RAY DIFFRACTIONf_dihedral_angle_d12.0362067
X-RAY DIFFRACTIONf_chiral_restr0.047864
X-RAY DIFFRACTIONf_plane_restr0.0041027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.551240.434281X-RAY DIFFRACTION2
1.61-1.650.733440.3648189X-RAY DIFFRACTION4
1.65-1.680.3039170.3189329X-RAY DIFFRACTION8
1.68-1.710.435220.3522477X-RAY DIFFRACTION15
1.73-1.760.3084380.3238676X-RAY DIFFRACTION25
1.76-1.80.3491770.27781618X-RAY DIFFRACTION38
1.8-1.850.25061120.24292100X-RAY DIFFRACTION50
1.85-1.90.3807760.27191586X-RAY DIFFRACTION37
1.9-1.960.28391660.24253017X-RAY DIFFRACTION71
1.96-2.030.26681810.20964009X-RAY DIFFRACTION94
2.03-2.120.26542380.20924116X-RAY DIFFRACTION97
2.12-2.210.22972360.19524264X-RAY DIFFRACTION100
2.21-2.330.24321510.2012804X-RAY DIFFRACTION66
2.33-2.470.2282060.19434293X-RAY DIFFRACTION100
2.47-2.660.25922570.20364271X-RAY DIFFRACTION100
2.66-2.930.23122280.20724328X-RAY DIFFRACTION100
2.93-3.360.24472150.18714354X-RAY DIFFRACTION100
3.36-4.230.18922600.14864312X-RAY DIFFRACTION99
4.23-44.950.1962270.16574598X-RAY DIFFRACTION100
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)
10.60030.3344-0.32161.1022-0.06171.19270.01080.0287-0.0013-0.18840.028-0.2509-0.18760.165-0.03930.09550.00140.04030.0446-0.00470.1348-1.316215.5622-40.7088
22.22320.27470.21821.8987-0.08941.8574-0.0427-0.4419-0.12220.28440.02490.1131-0.0081-0.19650.00750.08290.01280.00560.15780.05420.1072-16.1625-5.4076-22.915
30.4545-1.19210.08363.187-0.63111.8828-0.0692-0.13110.05220.29050.1286-0.0304-0.1727-0.0471-0.06430.09970.00620.02370.0507-0.01660.1059-8.982915.8133-28.3264
40.84260.39720.13141.26330.05921.3475-0.00380.0245-0.1618-0.11960.0197-0.09020.08930.0595-0.01230.03410.01010.01610.0511-0.00860.0973-3.62550.2843-41.257
53.70651.01022.03235.73160.75984.08320.16880.1147-0.3562-0.3509-0.15170.08310.4363-0.5577-0.04430.1853-0.04970.05890.2145-0.040.1397-17.1315-22.0963-71.0621
60.86090.4028-0.64761.5898-0.33181.13550.11810.4696-0.0144-0.6485-0.05190.1024-0.7458-0.3446-0.15790.6334-0.01670.06540.23240.0896-0.0305-14.91412.1176-76.7731
70.86720.1551-0.30620.67780.40731.31860.10740.20380.4615-0.88590.19-0.4168-0.67350.1602-0.29970.7145-0.09460.25420.25520.01070.334-4.951213.0811-76.6252
81.44470.15860.02371.4302-0.7292.91550.12290.24970.1373-0.30060.01380.0846-0.4258-0.1827-0.11490.2670.04380.01230.1720.00950.1055-17.9757-0.3784-68.602
90.9773-0.3386-0.42110.95230.03740.88930.05920.34780.1987-0.93440.2137-0.2446-0.3364-0.1762-0.02740.8396-0.1350.24420.3637-0.08510.0599-8.9719-3.8143-88.5461
101.3624-0.08340.00360.3473-0.29722.2193-0.04470.3627-0.1762-0.61040.0256-0.2342-0.2066-0.0251-0.01170.354-0.03130.04810.2261-0.0981-0.0034-12.6474-12.4844-78.8338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 79 )
2X-RAY DIFFRACTION2chain 'B' and (resid 80 through 176 )
3X-RAY DIFFRACTION3chain 'B' and (resid 177 through 227 )
4X-RAY DIFFRACTION4chain 'B' and (resid 228 through 358 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2 through 26 )
6X-RAY DIFFRACTION6chain 'A' and (resid 27 through 115 )
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 176 )
8X-RAY DIFFRACTION8chain 'A' and (resid 177 through 239 )
9X-RAY DIFFRACTION9chain 'A' and (resid 240 through 307 )
10X-RAY DIFFRACTION10chain 'A' and (resid 308 through 358 )

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