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- PDB-9orb: X-ray diffraction structure of the CTX-M-14 beta-lactamase-avibac... -

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Basic information

Entry
Database: PDB / ID: 9orb
TitleX-ray diffraction structure of the CTX-M-14 beta-lactamase-avibactam complex an inhibitor cocktail-soaked crystal
ComponentsBeta-lactamase
KeywordsHYDROLASE / enzyme / beta-lactamase / inhibitor / complex
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 / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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 discovery 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.A. / Tang, Y. / Rodriguez, J.A.
History
DepositionMay 21, 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)56,6315
Polymers56,0012
Non-polymers6293
Water10,431579
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3633
Polymers28,0011
Non-polymers3622
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)45.210, 107.190, 47.920
Angle α, β, γ (deg.)90.00, 101.88, 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.04 Å3/Da / Density % sol: 39.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 1.4 M potassium phosphate pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 11, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→35.29 Å / Num. obs: 139145 / % possible obs: 98.6 % / Redundancy: 3.54 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Net I/σ(I): 23.87
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.44 % / Rmerge(I) obs: 0.034 / Mean I/σ(I) obs: 12.71 / Num. unique obs: 24375 / CC1/2: 0.992 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→35.29 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 15.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1753 3541 5 %
Rwork0.1523 --
obs0.1535 70844 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 39 579 4531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064140
X-RAY DIFFRACTIONf_angle_d0.9445658
X-RAY DIFFRACTIONf_dihedral_angle_d6.527615
X-RAY DIFFRACTIONf_chiral_restr0.083664
X-RAY DIFFRACTIONf_plane_restr0.009754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.21821360.16282610X-RAY DIFFRACTION98
1.52-1.540.19151420.14822703X-RAY DIFFRACTION99
1.54-1.570.18281390.14452629X-RAY DIFFRACTION98
1.57-1.590.16891410.14392696X-RAY DIFFRACTION99
1.59-1.620.19361410.14242677X-RAY DIFFRACTION98
1.62-1.640.18881410.15362665X-RAY DIFFRACTION100
1.64-1.670.18621420.15822700X-RAY DIFFRACTION99
1.67-1.710.19821410.15862674X-RAY DIFFRACTION100
1.71-1.740.17331410.15582681X-RAY DIFFRACTION99
1.74-1.780.17691430.15282712X-RAY DIFFRACTION100
1.78-1.820.1871420.14452709X-RAY DIFFRACTION100
1.82-1.870.1611420.13972687X-RAY DIFFRACTION100
1.87-1.920.22341410.17062684X-RAY DIFFRACTION99
1.92-1.970.19961410.17372677X-RAY DIFFRACTION99
1.97-2.040.18981420.14932698X-RAY DIFFRACTION100
2.04-2.110.16241410.14642687X-RAY DIFFRACTION100
2.11-2.190.15971440.14342727X-RAY DIFFRACTION100
2.19-2.290.24891390.21122664X-RAY DIFFRACTION99
2.29-2.410.17121430.1512710X-RAY DIFFRACTION100
2.41-2.560.17271420.15772701X-RAY DIFFRACTION100
2.56-2.760.18391420.15352697X-RAY DIFFRACTION100
2.76-3.040.18421430.15362723X-RAY DIFFRACTION100
3.04-3.480.15991440.14632723X-RAY DIFFRACTION100
3.48-4.380.13081430.12822717X-RAY DIFFRACTION100
4.38-35.290.13761450.14072752X-RAY DIFFRACTION100

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