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

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Basic information

Entry
Database: PDB / ID: 8cuq
TitleX-ray crystal structure of ADC-33 in complex with sulfonamidoboronic acid 6e
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-OZO / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
Revision 1.3Oct 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

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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
Water10,467581
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)43.320, 83.940, 204.460
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-OZO / 3-[(4R)-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.: 581 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
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: 1.55→52.91 Å / Num. obs: 109336 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Net I/σ(I): 11.6 / Num. measured all: 736079 / Scaling rejects: 89
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
1.55-1.596.71.9175335179340.3850.7972.0781100
6.93-52.915.60.033790214120.9980.0150.03632.399.7

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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: 1.55→51.12 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 5402 4.95 %
Rwork0.1856 103819 -
obs0.187 109221 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.21 Å2 / Biso mean: 28.8937 Å2 / Biso min: 12.69 Å2
Refinement stepCycle: final / Resolution: 1.55→51.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5545 0 48 584 6177
Biso mean--36.93 37.2 -
Num. residues----717
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
1.55-1.570.34541920.332833483540
1.57-1.590.34451770.31634173594
1.59-1.610.35032030.306434503653
1.61-1.630.31571530.289633673520
1.63-1.650.33511590.296734573616
1.65-1.670.27821630.268334563619
1.67-1.690.28311730.259333703543
1.69-1.720.30281830.256534863669
1.72-1.750.26841550.246534213576
1.75-1.770.25771970.233133933590
1.77-1.80.2571900.220334553645
1.8-1.840.25182000.213433553555
1.84-1.870.23821770.207934603637
1.87-1.910.22451870.203534113598
1.91-1.950.20931610.196934773638
1.95-20.25581830.201934183601
2-2.050.23711760.199634993675
2.05-2.10.23081600.193834253585
2.1-2.170.22211950.185534663661
2.17-2.240.22642040.178933993603
2.24-2.320.22231660.186734693635
2.32-2.410.21681820.185235033685
2.41-2.520.20141810.184334363617
2.52-2.650.21931950.193134583653
2.65-2.820.25011960.197534853681
2.82-3.030.22561840.191435083692
3.03-3.340.22071680.188435353703
3.34-3.820.17261690.163635373706
3.82-4.810.1651820.137536143796
4.81-51.120.15991910.15737443935

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