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- PDB-9orh: MicroED structure of the CTX-M-14 beta-lactamase-avibactam comple... -

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Basic information

Entry
Database: PDB / ID: 9orh
TitleMicroED structure of the CTX-M-14 beta-lactamase-avibactam complex from inhibitor cocktail-soaked crystals
ComponentsBeta-lactamase
KeywordsHYDROLASE / enzyme / beta-lactamase / MicroED / inhibitor / complex / cocktail
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 2 Å
AuthorsVlahakis, N. / Rodriguez, J.A. / Jacobs, L.M.C. / Chen, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1548924 United States
Howard Hughes Medical Institute (HHMI)HHMI-EPI United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
CitationJournal: To Be Published
Title: Combining MicroED and native mass spectrometry for structural discovery of enzyme-small molecules complexes
Authors: Vlahakis, N.W. / Flowers, C.W. / Liu, M. / Agdanowski, M. / Johnson, S. / Summers, J.A. / Jacobs, L.M.C. / Keyser, C. / Russell, P. / Rose, S. / Orlans, J. / Adhami, N. / Chen, Y. / Sawaya, ...Authors: Vlahakis, N.W. / Flowers, C.W. / Liu, M. / Agdanowski, M. / Johnson, S. / Summers, J.A. / Jacobs, L.M.C. / Keyser, C. / Russell, P. / Rose, S. / Orlans, J. / Adhami, N. / Chen, Y. / Sawaya, M.R. / Basu, S. / De Sanctis, D. / Chen, Y. / Wakatsuki, S. / Nelson, H.M. / Loo, J.A. / Tang, Y. / Rodriguez, J.A.
History
DepositionMay 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,2794
Polymers55,7452
Non-polymers5352
Water68538
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1402
Polymers27,8721
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1402
Polymers27,8721
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.900, 106.420, 47.520
Angle α, β, γ (deg.)90.00, 100.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 27872.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, BKL28_004840, BKL28_005521, BXT93_ ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, BKL28_004840, BKL28_005521, BXT93_06855, CR538_26855, E4K51_21070, EIA08_25160, ETN48_p0088, HL563_21800, HL563_23665, HLZ39_20540, HLZ39_26710, NY836_21775, pCT_085, pHK01_011, RCS101_P0028, RCS103_P0010, RCS30_P0082, RCS56_P0085, RCS60_P0031, RCS63_P0006, RCS65_P0008, RCS66_P0053, RCS68_P0054, SAMEA4362930_00013, SAMEA4363083_00099, SAMEA4370290_00046
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9L5C7, beta-lactamase
#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: CTX-M-14 beta-lactamase bound to avibactam / Type: COMPLEX
Details: Crystals were grown by hanging-drop vapor diffusion from drops of 25.7 mg/mL CTX-M-14 mixed 1:1 with crystallization solution (1.4 M potassium phosphate pH 7.9)
Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
EM crystal formationDetails: Crystals were grown by hanging-drop vapor diffusion from drops of 25.7 mg/mL CTX-M-14 mixed 1:1 with crystallization solution (1.4 M potassium phosphate pH 7.9)
Temperature: 293 K
Buffer solutionpH: 7.9 / Details: 1.4 M potassium phosphate pH 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Crystals were grown by hanging-drop vapor diffusion from drops of 25.7 mg/mL CTX-M-14 mixed 1:1 with crystallization solution (1.4 M potassium phosphate pH 7.9)
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: TFS TALOS F200C
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / C2 aperture diameter: 70 µm
Specimen holderTemperature (max): 100 K / Temperature (min): 100 K
Image recordingElectron dose: 0.09 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k)
EM diffraction shellResolution: 2→2.1 Å / Fourier space coverage: 95.6 % / Multiplicity: 3.47 / Num. of structure factors: 3848 / Phase residual: 30.8 °
EM diffraction statsFourier space coverage: 94.6 % / High resolution: 2 Å / Num. of intensities measured: 96106 / Num. of structure factors: 28065 / Phase error rejection criteria: NONE / Rmerge: 0.254

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
EM 3D crystal entity∠α: 90 ° / ∠β: 100.689 ° / ∠γ: 90 ° / A: 44.9 Å / B: 106.42 Å / C: 47.52 Å / Space group name: P21 / Space group num: 4
CTF correctionType: NONE
3D reconstructionResolution: 2 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingPDB-ID: 1YLT

1ylt


Accession code: 1YLT / Source name: PDB / Type: experimental model
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27.65 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 2804 10 %
Rwork0.1974 --
obs0.2021 28029 94.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0084046
ELECTRON CRYSTALLOGRAPHYf_angle_d1.1925515
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d7.498595
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.07654
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.01727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.33541450.26261298ELECTRON CRYSTALLOGRAPHY95
2.03-2.070.26811370.23831237ELECTRON CRYSTALLOGRAPHY95
2.07-2.110.28471420.24351274ELECTRON CRYSTALLOGRAPHY96
2.11-2.150.28311410.2291277ELECTRON CRYSTALLOGRAPHY96
2.15-2.20.31641390.23971247ELECTRON CRYSTALLOGRAPHY95
2.2-2.250.27771440.2351297ELECTRON CRYSTALLOGRAPHY96
2.25-2.310.30061390.24691244ELECTRON CRYSTALLOGRAPHY95
2.31-2.370.33141450.23441310ELECTRON CRYSTALLOGRAPHY95
2.37-2.440.27851370.22881227ELECTRON CRYSTALLOGRAPHY95
2.44-2.520.31961410.22641276ELECTRON CRYSTALLOGRAPHY95
2.52-2.610.27561400.22121258ELECTRON CRYSTALLOGRAPHY95
2.61-2.710.26231420.21721270ELECTRON CRYSTALLOGRAPHY95
2.71-2.840.2761430.21211290ELECTRON CRYSTALLOGRAPHY95
2.84-2.990.27091410.21711269ELECTRON CRYSTALLOGRAPHY95
2.99-3.170.25971380.21871245ELECTRON CRYSTALLOGRAPHY95
3.17-3.420.26761430.19031283ELECTRON CRYSTALLOGRAPHY95
3.42-3.760.2071400.16041252ELECTRON CRYSTALLOGRAPHY93
3.76-4.30.15721360.14181222ELECTRON CRYSTALLOGRAPHY92
4.3-5.420.15321370.13761237ELECTRON CRYSTALLOGRAPHY92
5.42-27.650.23471340.18941212ELECTRON CRYSTALLOGRAPHY89

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