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- PDB-9ehy: X-ray crystal structure of ADC-33 beta-lactamase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9ehy
TitleX-ray crystal structure of ADC-33 beta-lactamase in complex with ceftazidime in acyl and product forms
ComponentsBeta-lactamase
KeywordsHYDROLASE / lactamase / complex / cephalosporin / ceftazidime
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
: / ACYLATED CEFTAZIDIME / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsPowers, R.A. / Wallar, B.J. / Jarvis, H.R. / Ziegler, Z.X. / June, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI072219 United States
CitationJournal: Mbio / Year: 2025
Title: Resistance to oxyimino-cephalosporins conferred by an alternative mechanism of hydrolysis by the Acinetobacter -derived cephalosporinase-33 (ADC-33), a class C beta-lactamase present in ...Title: Resistance to oxyimino-cephalosporins conferred by an alternative mechanism of hydrolysis by the Acinetobacter -derived cephalosporinase-33 (ADC-33), a class C beta-lactamase present in carbapenem-resistant Acinetobacter baumannii (CR Ab ).
Authors: Powers, R.A. / Wallar, B.J. / Jarvis, H.R. / Ziegler, Z.X. / June, C.M. / Bethel, C.R. / Hujer, A.M. / Taracila, M.A. / Rudin, S.D. / Hujer, K.M. / Prati, F. / Caselli, E. / Bonomo, R.A.
History
DepositionNov 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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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)83,0705
Polymers81,6292
Non-polymers1,4403
Water7,296405
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7703
Polymers40,8151
Non-polymers9552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3002
Polymers40,8151
Non-polymers4851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.127, 84.055, 205.597
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-A1BIM / (2R)-2-[(R)-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}(carboxy)methyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / hydrolyzed ceftazidime without pyridine ring


Mass: 485.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19N5O8S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CAZ / ACYLATED CEFTAZIDIME


Mass: 469.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O7S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M succinate/phosphate/glycine, 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-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.57→102.799 Å / Num. obs: 79527 / % possible obs: 93.5 % / Redundancy: 7.9 % / CC1/2: 0.999 / Rpim(I) all: 0.026 / Net I/σ(I): 15
Reflection shellResolution: 1.57→1.725 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3975 / CC1/2: 0.723 / Rpim(I) all: 0.349 / % possible all: 58.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
XDSdata scaling
PHASERphasing
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→43.85 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 3992 5.08 %
Rwork0.1918 --
obs0.1932 78548 74.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5451 0 79 405 5935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085685
X-RAY DIFFRACTIONf_angle_d0.8897740
X-RAY DIFFRACTIONf_dihedral_angle_d13.602775
X-RAY DIFFRACTIONf_chiral_restr0.051856
X-RAY DIFFRACTIONf_plane_restr0.0061005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.590.313580.3099105X-RAY DIFFRACTION
1.59-1.610.464270.3095138X-RAY DIFFRACTION
1.61-1.630.4392150.3052217X-RAY DIFFRACTION
1.63-1.650.4028220.2928398X-RAY DIFFRACTION
1.65-1.670.3028330.275552X-RAY DIFFRACTION16
1.67-1.70.3233460.266801X-RAY DIFFRACTION24
1.7-1.720.2998690.29511328X-RAY DIFFRACTION38
1.72-1.750.3232870.29781809X-RAY DIFFRACTION
1.75-1.780.30741330.29412366X-RAY DIFFRACTION
1.78-1.810.29531600.2723047X-RAY DIFFRACTION
1.81-1.840.28191660.26073314X-RAY DIFFRACTION
1.84-1.880.29561630.28823493X-RAY DIFFRACTION
1.88-1.910.40081470.36972890X-RAY DIFFRACTION
1.91-1.960.49281520.42943023X-RAY DIFFRACTION
1.96-20.28791800.22583425X-RAY DIFFRACTION100
2-2.050.25971840.2183460X-RAY DIFFRACTION
2.05-2.110.28391770.22993397X-RAY DIFFRACTION
2.11-2.170.24421870.19853448X-RAY DIFFRACTION
2.17-2.230.23911700.19423222X-RAY DIFFRACTION
2.26-2.320.28191570.20012569X-RAY DIFFRACTION99
2.32-2.410.22172100.19493469X-RAY DIFFRACTION100
2.41-2.520.24091970.19353437X-RAY DIFFRACTION
2.52-2.650.22891780.19153473X-RAY DIFFRACTION
2.65-2.820.22711940.19443462X-RAY DIFFRACTION100
2.82-3.040.21381910.18943496X-RAY DIFFRACTION
3.04-3.340.22131820.1883534X-RAY DIFFRACTION
3.34-3.830.18421770.16233362X-RAY DIFFRACTION95
3.83-4.820.14992070.13443575X-RAY DIFFRACTION100
4.82-43.850.17791930.16813746X-RAY DIFFRACTION

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