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- PDB-8fqo: ADC-33 in complex with boronic acid transition state inhibitor MB076 -

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Basic information

Entry
Database: PDB / ID: 8fqo
TitleADC-33 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 / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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: 1.83 Å
AuthorsPowers, R.A. / Wallar, B.J. / June, C.M. / Fish, E.R.
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 1.4Oct 16, 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)82,4705
Polymers81,6292
Non-polymers8413
Water8,071448
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2833
Polymers40,8151
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1882
Polymers40,8151
Non-polymers3731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.857, 83.994, 200.949
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: 40814.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: ampC, BAA1790NC_1053, EP550_05490, EP560_12590, EQH48_05445
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7Y407, 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ADC-33 (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: 1.81→100.475 Å / Num. obs: 41365 / % possible obs: 92.4 % / Redundancy: 5.9 % / CC1/2: 0.99 / Rpim(I) all: 0.102 / Net I/σ(I): 5.9
Reflection shellResolution: 1.83→2.068 Å / Rmerge(I) obs: 1.163 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2069 / CC1/2: 0.479 / % possible all: 53.1

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Processing

Software
NameVersionClassification
PHENIXv1.19refinement
Aimlessv2.2.1data scaling
PHASERphasing
autoPROCv1.0.5data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0X

4u0x


Resolution: 1.83→64.44 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 2083 5.04 %0.5
Rwork0.2042 ---
obs0.2064 41351 63.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→64.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 53 448 6045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035757
X-RAY DIFFRACTIONf_angle_d0.5637839
X-RAY DIFFRACTIONf_dihedral_angle_d12.1612085
X-RAY DIFFRACTIONf_chiral_restr0.044867
X-RAY DIFFRACTIONf_plane_restr0.0041019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.870.3182120.2492122X-RAY DIFFRACTION3
1.87-1.920.200750.2335122X-RAY DIFFRACTION3
1.92-1.970.2954180.2586341X-RAY DIFFRACTION8
1.97-2.030.3602300.2727713X-RAY DIFFRACTION17
2.03-2.10.2628650.26561222X-RAY DIFFRACTION30
2.1-2.170.3335910.26371802X-RAY DIFFRACTION44
2.17-2.260.31971390.25512600X-RAY DIFFRACTION63
2.26-2.360.32121720.25953261X-RAY DIFFRACTION80
2.36-2.480.28462040.23663999X-RAY DIFFRACTION97
2.48-2.640.27192080.23114101X-RAY DIFFRACTION100
2.64-2.840.2672270.2314128X-RAY DIFFRACTION100
2.84-3.130.25952290.21764114X-RAY DIFFRACTION100
3.13-3.580.21612080.18614189X-RAY DIFFRACTION100
3.58-4.510.2182480.15814144X-RAY DIFFRACTION99
4.51-64.440.21432270.18184410X-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)
11.51050.4787-0.0461.79410.3511.13580.024-0.36780.18390.20980.00020.0833-0.11530.059-0.01570.12710.04410.00940.1808-0.04310.0908-12.6699-11.299664.6448
21.15760.1877-0.2492.0097-0.24631.0225-0.0169-0.14840.10990.01380.02230.0472-0.0183-0.00860.00790.06760.0034-0.01510.102-0.02020.0609-15.4243-10.721555.4051
32.1490.2977-0.16412.672-0.36363.4186-0.00920.40160.4974-0.3697-0.0293-0.2203-0.76780.5543-0.01720.3251-0.08510.02950.25560.08570.3665-1.911311.736920.6299
41.94750.2618-0.02261.11960.84381.73250.03220.3086-0.37090.1439-0.05010.06040.3773-0.02620.02080.18830.0215-0.00130.141-0.00030.1496-11.7147-17.270117.8199
50.8275-0.3174-0.4091.0710.6561.52110.05750.1112-0.09780.1370.0262-0.07640.14210.0483-0.06010.1397-0.0016-0.04030.16890.02120.0697-8.3682-14.085921.0924
61.3449-0.48620.67651.13261.09292.19550.20020.2588-0.32720.5422-0.11880.27130.9358-0.22410.01280.2757-0.06090.02080.1625-0.0420.1709-11.1448-12.340727.6563
71.3095-0.5210.07891.86510.85723.09390.18450.51220.0202-0.34240.0339-0.23090.05210.3671-0.23710.1451-0.0290.01240.39510.00410.12772.4123-6.736710.0455
80.39780.4368-0.46771.2506-0.17220.6972-0.00880.80050.4517-0.3801-0.03120.2385-0.1712-0.2454-0.12850.25220.0231-0.0220.54850.16970.2039-17.1366-2.66394.9191
91.05520.3814-0.5631.17210.10812.60430.10040.33990.7412-0.2783-0.0593-0.096-0.62290.1442-0.16810.2405-0.02260.03470.22090.27290.2637-8.56954.540415.2746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 195 )
2X-RAY DIFFRACTION2chain 'B' and (resid 196 through 360 )
3X-RAY DIFFRACTION3chain 'A' and (resid 3 through 44 )
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 136 )
5X-RAY DIFFRACTION5chain 'A' and (resid 137 through 208 )
6X-RAY DIFFRACTION6chain 'A' and (resid 209 through 225 )
7X-RAY DIFFRACTION7chain 'A' and (resid 226 through 257 )
8X-RAY DIFFRACTION8chain 'A' and (resid 258 through 308 )
9X-RAY DIFFRACTION9chain 'A' and (resid 309 through 359 )

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