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Basic information

Entry
Database: PDB / ID: 9top
TitleContaminated room temperature serial crystal structure of CTX-M-15 class A beta-lactamase, drop on fixed target at DLS, 2.6 s 'control' contaminated with 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. / 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
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.175, 45.798, 118.622
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, 205 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.: 200 / 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: 43.28 %
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→59.32 Å / Num. obs: 23430 / % possible obs: 99.41 % / Redundancy: 13.45 % / Biso Wilson estimate: 18.91 Å2 / CC1/2: 0.865 / R split: 0.3 / Net I/σ(I): 2.179
Reflection shellResolution: 1.8→1.831 Å / Mean I/σ(I) obs: 0.842 / Num. unique obs: 1147 / CC1/2: 0.285 / R split: 0.841 / % possible all: 98.37
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: 3058

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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→59.31 Å / SU ML: 0.2306 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2294 1163 5 %
Rwork0.1885 22108 -
obs0.1905 23271 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→59.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 37 200 2193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622136
X-RAY DIFFRACTIONf_angle_d0.82532916
X-RAY DIFFRACTIONf_chiral_restr0.0514334
X-RAY DIFFRACTIONf_plane_restr0.007386
X-RAY DIFFRACTIONf_dihedral_angle_d12.4154816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.30241400.27042625X-RAY DIFFRACTION95.41
1.88-1.980.32611410.25132689X-RAY DIFFRACTION97.62
1.98-2.110.31381450.23422687X-RAY DIFFRACTION98.47
2.11-2.270.26411480.21162765X-RAY DIFFRACTION99.59
2.27-2.50.23731390.19292761X-RAY DIFFRACTION99.45
2.5-2.860.25511450.18412785X-RAY DIFFRACTION99.59
2.86-3.60.19171500.16252825X-RAY DIFFRACTION99.93
3.6-59.310.17461550.15992971X-RAY DIFFRACTION99.71
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)
12.920155363821.31377979699-1.782836034191.94699498464-1.551782761764.34263674619-0.16413600180.477467571694-0.449544683315-0.4672983436140.0475153358328-0.4458417775080.6656198584140.1539733470270.105471144530.242594109550.004644974077950.03302192430650.221200424637-0.02526254897410.2268867041125.29678144703-20.57138180953.36595062438
22.10262919597-0.622369227019-0.8018355342311.565475720610.4397243055781.33846184258-0.0696729438127-0.126896190243-0.00362131747880.06243653918340.0906509360286-0.01352888912110.1149533233640.1780280099730.01204230904270.127221253634-0.00537587884736-0.01379208855810.1154433533840.01144929355220.0792726511908-1.74448507893-14.764061541321.0129731579
33.382043453690.943052049712-1.342871046577.19099674593-2.446348276184.656315431820.189005031784-0.1327116627070.2486276589770.7865573919160.07857071629350.51465538451-0.237439965902-0.170820952092-0.231734047240.254634782446-0.06158499040190.02789250268110.151159979935-0.0469849202090.219848183392-17.28507434082.657669781130.7754214409
43.75428397845-0.536646524669-0.4293620798455.108606413250.7085013792833.698680323170.002742834989860.234174451097-0.0203190192387-0.2272319099390.03908619906870.398703857748-0.2693625280770.000891011870836-0.04371860498630.102265660865-0.0190486117144-0.01842864886540.1528190166260.005268779126590.196621018012-17.06177427382.3026347220.1338812185
52.73349069635-2.094386909280.8666150880842.77975053085-0.8805632215071.560839010520.120824487081-0.0609198515539-0.04710245033740.0274398541865-0.04776960286120.1298338411990.03840532985730.0217170577704-0.03908430500280.109653919129-0.03056934830610.01274381175330.140733466421-0.002005740706170.138340045904-5.83322901251-3.2843032096627.1286296181
60.784933582854-0.11032773075-0.09041897277111.262025402230.3368924682961.63754727978-0.02703409086720.00921826996538-0.0322181049716-0.03349954211670.05678191314150.03479554877820.0744555890962-0.00341605804316-0.02005163236080.1171426411880.00865231597274-0.0008178417516430.1161119530760.004766497244340.100061346862-5.24267984843-12.875788144718.0167277778
74.269906864153.53250756926-1.377118564945.97590898904-1.976296320392.788668676410.02591333087010.1877070225320.000564566381962-0.08556939551410.07147728025310.07778891824860.144918841475-0.010647718019-0.1304931529620.152914517866-0.002568546167980.009924587040090.137104278148-0.03395450713010.0917519124875-2.88235746657-15.60564487267.8988272837
86.86941392603-1.710872565460.115669603722.44925972647-1.867793319567.46470025419-0.00737413340680.432074117625-0.435505080259-0.4992432062180.1058917541680.2859457712490.446995335329-0.199160468987-0.03873762137670.197094185213-0.0429780779583-0.009505696717280.236869055026-0.08084521969990.16697175498-4.05256393982-21.00428290743.63010577312
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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