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- PDB-9to5: Room temperature serial crystal structure of CTX-M-15 class A bet... -

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Basic information

Entry
Database: PDB / ID: 9to5
TitleRoom temperature serial crystal structure of CTX-M-15 class A beta-lactamase uncomplexed resting state from Diamond Light Source
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance / beta-lactamase / inhibitor / dynamics / tr-SFX / XFEL
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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.73 Å
AuthorsHinchliffe, P. / Tooke, C.L. / 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 16, 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)28,4474
Polymers28,2931
Non-polymers1553
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-37 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.196, 45.697, 118.358
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

#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
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.05 %
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: 0.9998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.73→59.18 Å / Num. obs: 26359 / % possible obs: 99.95 % / Redundancy: 34.42 % / Biso Wilson estimate: 18.06 Å2 / CC1/2: 0.956 / R split: 0.174 / Net I/σ(I): 3.547
Reflection shellResolution: 1.73→1.7598 Å / Mean I/σ(I) obs: 1.341 / Num. unique obs: 1287 / CC1/2: 0.594 / R split: 0.453
Serial crystallography sample deliveryDescription: silicon 'Oxford' chip / Method: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: Mylar film

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.73→59.18 Å / SU ML: 0.1843 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.6813
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1886 1369 5.19 %
Rwork0.1579 24984 -
obs0.1594 26353 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.95 Å2
Refinement stepCycle: LAST / Resolution: 1.73→59.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 7 186 2136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912013
X-RAY DIFFRACTIONf_angle_d1.04372740
X-RAY DIFFRACTIONf_chiral_restr0.0565319
X-RAY DIFFRACTIONf_plane_restr0.0062362
X-RAY DIFFRACTIONf_dihedral_angle_d16.8115755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.790.28461440.23982432X-RAY DIFFRACTION99.57
1.79-1.860.24541110.2052459X-RAY DIFFRACTION99.96
1.86-1.950.19971360.17492482X-RAY DIFFRACTION99.96
1.95-2.050.19851510.16222447X-RAY DIFFRACTION100
2.05-2.180.19621580.1542440X-RAY DIFFRACTION100
2.18-2.350.19761380.14412470X-RAY DIFFRACTION100
2.35-2.580.18471320.14642505X-RAY DIFFRACTION100
2.58-2.960.18071270.14942513X-RAY DIFFRACTION99.96
2.96-3.730.16091390.14582556X-RAY DIFFRACTION99.96
3.73-59.180.17971330.15672680X-RAY DIFFRACTION99.89
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)
12.585520939931.91276622143-1.72428103824.31250365084-1.938411143693.52458246467-0.2197677162850.374177753639-0.334063279437-0.5048163554150.0958898413326-0.3055667865350.535913659460.0833178370370.09732158730060.2035892726950.01047152122640.0322856601310.176959125964-0.03835979214590.1735384848735.36624846158-20.47593743154.00018683984
22.474796220120.86096329343-0.1869351871983.352386730170.1223747174981.1963548365-0.0465062180063-0.154977971563-0.3370077976660.0864750057376-0.0691385459215-0.2682130215710.2874559246610.1438904529950.1184201853720.1648315050870.02255173319160.02752580925170.1370692002230.03566549832980.1062660515244.72751985678-20.284996891414.9095591203
32.40047036221-0.623996468455-0.1612448663092.88507915366-0.6355583549991.96240242947-0.0508016766304-0.4537298449690.1503725135560.4482165243850.2057975513410.239106494138-0.0165365030346-0.0618352301847-0.1171514507150.179977296704-0.01771078059770.02510468269020.153538205373-0.03126524507290.134280155378-12.1941617275-5.8282857754229.7181866405
42.4596988147-2.48409713661-3.431541439022.569208125513.606239645559.08318849210.0567522286630.2780831422160.284848057413-0.398044141363-0.1104757272860.491414318642-0.5015378047930.02604864161930.1032729328240.233715428952-0.00282822644908-0.03118064392920.1777288227270.02241600652360.276623126292-15.92613014978.0866170804918.6521590258
51.43534905484-0.317113375521-0.297634587271.793539654680.1693055664971.072235195860.023598402743-0.05324638230470.05656721559860.03316238478210.001191552083160.0432203717015-0.003470433110630.0310506668093-0.01761960873380.110568072038-0.01131438451638.39979135318E-50.119775460552-0.01115669878610.0937147855559-3.0620318978-5.8827566016823.0069676978
65.13100064684-2.052707395910.9005582453622.97616610163-0.2698960042164.11211922619-0.0497693936704-0.161201175376-0.3307006819520.1726825638280.1889199858040.3110441361730.0176628576853-0.143446567536-0.1052901087070.149793222829-0.03675645098640.02234295841390.1203413829060.005757903129810.158553720396-14.4171929408-16.98087755825.7533575441
72.084709736380.487016788548-0.09854063041.4412546420.4452209011681.946585778240.04667819962580.0028306551550.000352635314658-0.129890367694-0.06139843766450.1541793206860.0572456375164-0.1294678557390.01229731900240.1137815735470.00618434029519-0.01594723247350.0948763856339-0.001139101708730.110392810883-8.96982647886-14.63578846719.73466392969
86.26251298343.15813187044-2.284818568594.14753313879-2.155973192312.58636598296-0.01173512893120.155236937334-0.234374348925-0.2644926514230.1461678820530.2359037265990.395637174487-0.0491342963803-0.1395495806360.212881124331-0.0111413065326-0.02952350490480.110503776102-0.0250370428460.121357882888-5.75987414446-22.272226415912.0017671049
96.449185778264.90632018292-0.9594916691424.61276182705-1.93513588483.70019686995-0.04633108551520.3431878157050.172666708689-0.3497157008070.1918012853620.2467743097750.0733480424869-0.0701849590099-0.1534728383550.1642447317320.02511788559480.01688575255520.149213649445-0.02721934123890.0717092217247-0.614464883492-12.51484651412.27319821809
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 68 )52 - 6825 - 41
33chain 'A' and (resid 69 through 96 )69 - 9642 - 70
44chain 'A' and (resid 97 through 115 )97 - 11571 - 89
55chain 'A' and (resid 116 through 194 )116 - 19490 - 172
66chain 'A' and (resid 195 through 213 )195 - 213173 - 191
77chain 'A' and (resid 214 through 250 )214 - 250192 - 230
88chain 'A' and (resid 251 through 264 )251 - 264231 - 244
99chain 'A' and (resid 265 through 287 )265 - 287245 - 267

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