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- PDB-9tov: Room temperature serial crystal structure of AmpC class C beta-la... -

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Basic information

Entry
Database: PDB / ID: 9tov
TitleRoom temperature serial crystal structure of AmpC class C beta-lactamase, drop on fixed target from PAL-XFEL, 80 ms mixed with avibactam
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance / beta-lactamase / inhibitor / dynamics / tr-SFX / XFEL
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-NXL / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 3.5 Å
AuthorsHinchliffe, P. / Freeman, E.I. / Lang, P.A. / Rabe, P. / Kamps, J.G.A. / Aller, P. / Schofield, C.J. / Orville, A.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101021207European Union
CitationJournal: Iucrj / Year: 2026
Title: Drop-on-fixed-target reaction initiation approach for serial and time-resolved crystallography.
Authors: Kamps, J.J.A.G. / Hinchliffe, P. / Glerup, J. / Freeman, E.I. / Lang, P.A. / Tooke, C.L. / Beer, M. / Parkinson, L. / Gu, D.H. / Park, S. / Devenish, N. / Zhou, T. / Shilova, A. / Kaur, S. / ...Authors: Kamps, J.J.A.G. / Hinchliffe, P. / Glerup, J. / Freeman, E.I. / Lang, P.A. / Tooke, C.L. / Beer, M. / Parkinson, L. / Gu, D.H. / Park, S. / Devenish, N. / Zhou, T. / Shilova, A. / Kaur, S. / Rabe, P. / Schofield, C.J. / Spencer, J. / Park, J. / Owen, R.L. / Orville, A.M. / Aller, P.
History
DepositionDec 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: 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)79,4433
Polymers79,1762
Non-polymers2671
Water66737
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8552
Polymers39,5881
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,5881
Polymers39,5881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.070, 77.836, 99.306
Angle α, β, γ (deg.)90.000, 116.453, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 4 through 8 or resid 10...
d_2ens_1(chain "B" and (resid 4 through 8 or resid 10 through 323 or resid 325 through 361))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAILEILEAA4 - 81 - 5
d_12ASPASPASNASNAA10 - 2897 - 286
d_13LEULEUGLYGLYAA293 - 323290 - 320
d_14TYRTYRGLNGLNAA325 - 361322 - 358
d_21ALAALAILEILEBB4 - 81 - 5
d_22ASPASPGLYGLYBB10 - 3237 - 320
d_23TYRTYRGLNGLNBB325 - 361322 - 358

NCS oper: (Code: givenMatrix: (-0.99743075672, -0.0694968336484, -0.0173803240126), (-0.0715633692233, 0.977643590908, 0.197716193927), (0.00325111293985, 0.198452007469, -0.980105214248)Vector: 90. ...NCS oper: (Code: given
Matrix: (-0.99743075672, -0.0694968336484, -0.0173803240126), (-0.0715633692233, 0.977643590908, 0.197716193927), (0.00325111293985, 0.198452007469, -0.980105214248)
Vector: 90.8827859262, -0.827765602488, 41.7208497302)

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Components

#1: Protein Beta-lactamase / Cephalosporinase / CSase


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ampC, ampA, b4150, JW4111 / Production host: Escherichia coli (E. coli) / References: UniProt: P00811, 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.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: batch mode
Details: Potassium phosphate (1.9 M, pH 8.8) with crystal seed

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.3042 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jun 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3042 Å / Relative weight: 1
ReflectionResolution: 3.5→59.18 Å / Num. obs: 10398 / % possible obs: 99.97 % / Redundancy: 37.97 % / Biso Wilson estimate: 43.9 Å2 / CC1/2: 0.683 / R split: 0.206 / Net I/σ(I): 3.818
Reflection shellResolution: 3.5→3.5604 Å / Redundancy: 16.64 % / Mean I/σ(I) obs: 2.917 / Num. unique obs: 516 / CC1/2: 0.132 / R split: 0.383 / % possible all: 100
Serial crystallography sample deliveryDescription: silicon 'Oxford' chip / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Drop on fixed target
Serial crystallography data reductionLattices indexed: 3117

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.5→45.55 Å / SU ML: 0.3432 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.1789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2198 519 5.01 %
Rwork0.1302 9843 -
obs0.1346 10362 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.8 Å2
Refinement stepCycle: LAST / Resolution: 3.5→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 17 37 5630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01215762
X-RAY DIFFRACTIONf_angle_d1.25477875
X-RAY DIFFRACTIONf_chiral_restr0.0641854
X-RAY DIFFRACTIONf_plane_restr0.00831014
X-RAY DIFFRACTIONf_dihedral_angle_d15.12752088
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.940398610551 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.850.25831270.14962420X-RAY DIFFRACTION99.3
3.85-4.410.21761300.12222442X-RAY DIFFRACTION99.57
4.41-5.550.19951290.11392464X-RAY DIFFRACTION99.92
5.55-45.550.21271330.13922517X-RAY DIFFRACTION99.92

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