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Basic information

Entry
Database: PDB / ID: 9too
TitleContaminated room temperature serial crystal structure of CTX-M-15 class A beta-lactamase, drop on fixed target at DLS, 2.6 s mixed with 200 mM avibactam
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance / beta-lactamase / inhibitor / dynamics / tr-SSX
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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-FYG / Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsParkinson, L. / Tooke, C.L. / Hinchliffe, P. / Beer, M. / Kamps, J.A.G. / Spencer, J.
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9076
Polymers28,2931
Non-polymers6145
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.178, 45.822, 118.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 28292.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Solu / References: UniProt: G3G192, beta-lactamase

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Non-polymers , 5 types, 219 molecules

#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: Chemical ChemComp-FYG / (2S,5R)-7-oxo-6-(sulfooxy)-1,6-diazabicyclo[3.2.1]octane-2-carboxamide / Avibactam


Mass: 265.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 2.0 M ammonium sulphate, 0.1 M Tris 8.0, with crystal seed

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.8→59.33 Å / Num. obs: 23440 / % possible obs: 99.39 % / Redundancy: 14.49 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.796 / R split: 0.308 / Net I/σ(I): 2.173
Reflection shellResolution: 1.8→1.831 Å / Redundancy: 8.72 % / Mean I/σ(I) obs: 0.829 / Num. unique obs: 1147 / CC1/2: 0.287 / R split: 0.791 / % possible all: 98.62
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: 3263

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→59.32 Å / SU ML: 0.2785 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.1193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 1165 5.01 %
Rwork0.1879 22092 -
obs0.1899 23257 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.78 Å2
Refinement stepCycle: LAST / Resolution: 1.8→59.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 37 214 2207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062121
X-RAY DIFFRACTIONf_angle_d0.83552895
X-RAY DIFFRACTIONf_chiral_restr0.0515333
X-RAY DIFFRACTIONf_plane_restr0.0061383
X-RAY DIFFRACTIONf_dihedral_angle_d12.4343809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.37351360.28832613X-RAY DIFFRACTION94.92
1.88-1.980.30721390.25492680X-RAY DIFFRACTION97.24
1.98-2.110.28311420.22432694X-RAY DIFFRACTION98.47
2.11-2.270.23221450.20852760X-RAY DIFFRACTION99.32
2.27-2.50.24841480.19442760X-RAY DIFFRACTION99.42
2.5-2.860.23821500.1882786X-RAY DIFFRACTION99.83
2.86-3.60.22261470.15882827X-RAY DIFFRACTION99.8
3.6-59.320.1671580.15732972X-RAY DIFFRACTION99.81
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.499291734751.21611662109-1.565306074971.99488972533-1.349304042084.11413535507-0.1864777825920.492801327007-0.349887993625-0.2704672481160.0806450285271-0.5926003223380.580548995806-0.06008061100170.08379271969520.234533861883-0.001336248848740.04080197653910.23714556735-0.04257635065190.2465791850185.27371565576-20.59899168573.36050325738
22.0043321543-0.638009262166-0.7718808942241.392257331190.237136620181.2905403254-0.0682070037855-0.120273850053-0.007512110583620.07914448702970.0352896310712-0.08253963871950.1166210038590.1669928148820.01128394085620.163356770479-0.0180624561037-0.01371708483740.1401073153990.006956225578430.118532096246-1.76569180213-14.771756065921.0351443435
33.025718424231.04279008786-1.272130506076.72123209796-2.300517798734.161114927260.168744676367-0.1773580687620.2053702673460.7533905604020.0352058724770.415421332424-0.325882320759-0.0985766463197-0.2247248305190.235537279285-0.02901908949410.02958301621090.181296285183-0.05980360315780.246738062509-17.30686367882.6465809652630.7807893161
43.52878282236-0.631251840506-0.4189901243034.947026907930.7057478175053.698630224940.05236147504260.128755593071-0.0886692531321-0.2520105685780.02982438887240.481517638793-0.227283195972-0.215766472903-0.04694781380020.138668001122-0.0136498817254-0.01702001415160.153820234616-0.0008330964135840.179757807792-17.0639065642.2912305144120.1357895695
52.60053525779-2.01086679230.9739655789022.59494932576-0.9379791478131.731128210810.0930958837219-0.0820985428456-0.09868787595930.1742214102930.005015745744750.2310244936930.01200589547320.0027837253739-0.05305314167320.142942257302-0.02286233122820.0152006919950.159490033092-0.01289943935010.168473735881-5.59901730216-3.5192814009426.8954749839
60.86257511026-0.0786215377531-0.1850788684761.068861775810.2355051617721.57052909339-0.0160810325665-0.0404239509755-0.0437755140495-0.009741624774580.01194844826410.1045903630590.1085416303330.0182662787016-0.02040841002160.1433494822980.0006988884682020.002811756388390.1235798559790.002954252843460.135886181849-5.24414778612-12.881876789118.027772377
74.270359275273.59398471346-1.392571823895.95596537738-1.943975845422.740112108730.07846218122740.07880349782520.00729244028001-0.305993464578-0.05599151187670.2000367055730.0712952235696-0.0128741556084-0.1291717955110.1934756658010.00736875162162-0.01090383947480.157682957169-0.04975974011870.0997283880163-2.88077636148-15.62489807767.88719265909
86.98438712222-1.373444411110.2752452814346.7068197704-1.170236402966.965000981420.04280569678390.399152190442-0.418493555372-0.396338594190.04965226947460.2814195764320.485366986297-0.0454732472388-0.02736095678340.203095810009-0.03709152578860.00105732611940.218064506586-0.0754961920370.118664833126-4.03764915255-21.0266516513.63627837952
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 51 )28 - 511 - 24
22chain 'A' and (resid 52 through 86 )52 - 8625 - 59
33chain 'A' and (resid 87 through 101 )87 - 10160 - 74
44chain 'A' and (resid 102 through 128 )102 - 12875 - 101
55chain 'A' and (resid 129 through 155 )129 - 155102 - 128
66chain 'A' and (resid 156 through 250 )156 - 250129 - 223
77chain 'A' and (resid 251 through 273 )251 - 273224 - 246
88chain 'A' and (resid 274 through 288 )274 - 288247 - 261

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