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- PDB-8cup: X-ray crystal structure of ADC-33 in complex with sulfonamidoboro... -

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Basic information

Entry
Database: PDB / ID: 8cup
TitleX-ray crystal structure of ADC-33 in complex with sulfonamidoboronic acid 6d
ComponentsBeta-lactamase
KeywordsHYDROLASE/Inhibitor / Cephalasporinase / Inhibitor / 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
Chem-OZF / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsFernando, M.C. / Wallar, B.J. / Powers, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI072219 United States
CitationJournal: Antibiotics / Year: 2023
Title: Sulfonamidoboronic Acids as "Cross-Class" Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat ...Title: Sulfonamidoboronic Acids as "Cross-Class" Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat Resistance in Acinetobacter baumannii .
Authors: Introvigne, M.L. / Beardsley, T.J. / Fernando, M.C. / Leonard, D.A. / Wallar, B.J. / Rudin, S.D. / Taracila, M.A. / Rather, P.N. / Colquhoun, J.M. / Song, S. / Fini, F. / Hujer, K.M. / ...Authors: Introvigne, M.L. / Beardsley, T.J. / Fernando, M.C. / Leonard, D.A. / Wallar, B.J. / Rudin, S.D. / Taracila, M.A. / Rather, P.N. / Colquhoun, J.M. / Song, S. / Fini, F. / Hujer, K.M. / Hujer, A.M. / Prati, F. / Powers, R.A. / Bonomo, R.A. / Caselli, E.
History
DepositionMay 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.pdbx_database_id_PubMed ..._citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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)82,3914
Polymers81,6292
Non-polymers7622
Water12,394688
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1962
Polymers40,8151
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1962
Polymers40,8151
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.290, 83.820, 203.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-OZF / 3-[(4S)-4-ethyl-5,7,7-trihydroxy-2,2,7-trioxo-6-oxa-2lambda~6~-thia-3-aza-7lambda~5~-phospha-5-boraheptan-1-yl]benzoic acid


Mass: 381.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17BNO9PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25% w/v PEG 1500 0.1 M succinate/phosphate/glycine buffer pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.54→43.47 Å / Num. obs: 110715 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 20.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Net I/σ(I): 11.8 / Num. measured all: 799219 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.54-1.587.31.995899680750.3710.7892.1421100
6.89-43.476.10.031869214310.9990.0130.03435.599.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo ADC-33

Resolution: 1.54→43.47 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 5557 5.02 %
Rwork0.1835 105050 -
obs0.1852 110607 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.67 Å2 / Biso mean: 26.4781 Å2 / Biso min: 11.03 Å2
Refinement stepCycle: final / Resolution: 1.54→43.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5578 0 39 699 6316
Biso mean--33.25 35.69 -
Num. residues----718
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.54-1.560.3451920.318434603652
1.56-1.580.29141860.292834333619
1.58-1.60.30242080.293734503658
1.6-1.620.31041890.286634453634
1.62-1.640.32131810.280234233604
1.64-1.660.32711770.279335113688
1.66-1.680.31021700.287934473617
1.68-1.710.34841890.276834303619
1.71-1.730.30231830.267435223705
1.73-1.760.29521680.24934343602
1.76-1.790.28961880.226634833671
1.79-1.830.25611980.224634663664
1.83-1.860.25281830.202834813664
1.86-1.90.26991910.202334393630
1.9-1.940.2151650.193634913656
1.94-1.990.21892000.195734813681
1.99-2.040.22671920.199634723664
2.04-2.090.26441850.203334893674
2.09-2.150.2161770.175335143691
2.15-2.220.21881840.173434663650
2.22-2.30.19571700.17235323702
2.3-2.390.20781970.177134983695
2.39-2.50.24761880.171734833671
2.5-2.630.18611870.174635243711
2.63-2.80.22341810.177735353716
2.8-3.010.24461870.184835413728
3.01-3.320.19361860.174135693755
3.32-3.80.18881850.161335773762
3.8-4.780.14491820.134636413823
4.79-43.470.18781880.165938134001

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