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- PDB-9ors: MicroED structure of CTX-M-14 beta-lactamase co-crystallized with... -

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Basic information

Entry
Database: PDB / ID: 9ors
TitleMicroED structure of CTX-M-14 beta-lactamase co-crystallized with avibactam
ComponentsBeta-lactamase
KeywordsHYDROLASE / Enzyme / beta-lactamase / inhibitor / complex / MicroED
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.W. / Rodriguez, J.A. / Jacobs, L.M.C. / Chen, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)HHMI-EPI United States
National Science Foundation (NSF, United States)DMR-1548924 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 discovert of enzyme-small molecule 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. / 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)56,5364
Polymers56,0012
Non-polymers5352
Water57632
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2682
Polymers28,0011
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2682
Polymers28,0011
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.800, 105.780, 47.680
Angle α, β, γ (deg.)90.00, 100.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 28000.547 Da / Num. of mol.: 2 / Fragment: UNP residues 23-284
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, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, AM340_ ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, AM340_28340, AM465_01285, AM465_06510, AM465_23360, APT94_14605, BEN53_26220, BJJ90_27545, BK334_27290, BOH76_00730, BON63_16015, BON65_15195, BON66_01305, BON69_22545, BON72_03470, BON75_10525, BON76_14325, BON83_15455, BON86_08515, BON91_02075, BON92_04750, BON94_23850, BON95_01680, BON96_03940, BON98_23175, BXT93_06855, C5N07_28500, CDL37_21060, CR538_26855, DW236_20870, E4K51_21070, EIA08_25160, EIA21_26975, ELT23_05930, ELV24_09995, ELX61_24095, EST51_15935, EST51_18575, EST51_22260, EST51_22365, ETN48_p0088, FNJ69_13810, FTV90_03295, GE096_24920, GE096_25355, GQE36_23945, HGR36_01450, HGR36_27140, HHH24_004455, HHH24_005319, HJI79_003882, HJI79_004995, HK427_004976, HK427_005087, HL152_24835, HL152_25835, HL563_21800, HL563_23665, HLT96_25270, HLT96_28700, HLU13_27785, HLY53_18605, HLY53_26190, HLZ85_26065, HMW26_20895, HMW26_29355, HNC73_28650, HNC75_27190, HNC75_29165, HNC80_26145, HNC80_27675, HNC88_26185, HNC88_27880, HND23_26750, HND23_28285, HNV91_23425, HNV91_24920, HNV94_24095, HNV94_27845, pCT_085, pHK01_011, RCS103_P0010, RCS30_P0082, RCS56_P0085, RCS60_P0031, RCS63_P0006, RCS65_P0008, RCS66_P0053, SAMEA4362930_00013, SAMEA4363083_00099, SAMEA4370290_00046, WP4S18E07_P40650, WP7S17E01_P10270, WP7S18E09_37980
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.: 32 / 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
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)
Image scansWidth: 4096 / Height: 4096
EM diffraction shellResolution: 2→2.1 Å / Fourier space coverage: 84.4 % / Multiplicity: 6.7 / Num. of structure factors: 3386 / Phase residual: 31.7 °
EM diffraction statsFourier space coverage: 83.7 % / High resolution: 2 Å / Num. of intensities measured: 164695 / Num. of structure factors: 24699 / Phase error rejection criteria: NONE / Rmerge: 0.291

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
EM software
IDNameCategory
8PHENIXmolecular replacement
13PHENIXmodel refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 100.957 ° / ∠γ: 90 ° / A: 44.8 Å / B: 105.79 Å / C: 47.68 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→46.81 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 2469 10 %
Rwork0.2029 --
obs0.2081 24689 83.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.73 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0054025
ELECTRON CRYSTALLOGRAPHYf_angle_d1.0455485
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d6.775590
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.055651
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.011723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.30461390.24991254ELECTRON CRYSTALLOGRAPHY84
2.04-2.080.30491360.24611219ELECTRON CRYSTALLOGRAPHY84
2.08-2.130.32381380.25051241ELECTRON CRYSTALLOGRAPHY84
2.13-2.170.32251380.2451243ELECTRON CRYSTALLOGRAPHY85
2.17-2.230.30611380.23741240ELECTRON CRYSTALLOGRAPHY84
2.23-2.290.30591350.24741221ELECTRON CRYSTALLOGRAPHY84
2.29-2.360.32151400.24381260ELECTRON CRYSTALLOGRAPHY84
2.36-2.430.29111370.2291230ELECTRON CRYSTALLOGRAPHY84
2.43-2.520.28611390.23861248ELECTRON CRYSTALLOGRAPHY84
2.52-2.620.29931350.24031223ELECTRON CRYSTALLOGRAPHY84
2.62-2.740.30551380.23421238ELECTRON CRYSTALLOGRAPHY84
2.74-2.880.3021370.23891237ELECTRON CRYSTALLOGRAPHY84
2.88-3.060.2781390.22691244ELECTRON CRYSTALLOGRAPHY85
3.06-3.30.28431370.21561237ELECTRON CRYSTALLOGRAPHY84
3.3-3.630.24541380.18051244ELECTRON CRYSTALLOGRAPHY84
3.63-4.160.20621370.15981227ELECTRON CRYSTALLOGRAPHY83
4.16-5.240.15591340.12661213ELECTRON CRYSTALLOGRAPHY82
5.24-46.810.1811340.16471201ELECTRON CRYSTALLOGRAPHY80

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