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- PDB-9g80: CTX-M-14 mixed with piperacillin at 3s delay time - serial crysta... -

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Basic information

Entry
Database: PDB / ID: 9g80
TitleCTX-M-14 mixed with piperacillin at 3s delay time - serial crystallography temperature series; 20C, 293K
ComponentsBeta-lactamase
KeywordsHYDROLASE / catalytic activity / beta-lactamase activity / hydrolase activity
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
Piperacillin / Hydrolyzed piperacillin / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPrester, A. / von Stetten, D. / Mehrabi, P. / Schulz, E.C.
Funding support Germany, European Union, 4items
OrganizationGrant numberCountry
Joachim Herz StiftungBiomedical physics of infection Germany
German Research Foundation (DFG)458246365 Germany
German Federal Ministry for Education and Research01KI2114 Germany
European CommissionEuropean Union
CitationJournal: Nat Commun / Year: 2025
Title: Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography.
Authors: Schulz, E.C. / Prester, A. / von Stetten, D. / Gore, G. / Hatton, C.E. / Bartels, K. / Leimkohl, J.P. / Schikora, H. / Ginn, H.M. / Tellkamp, F. / Mehrabi, P.
History
DepositionJul 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1584
Polymers31,0091
Non-polymers1,1493
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10860 Å2
Unit cell
Length a, b, c (Å)42.150, 42.150, 234.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Beta-lactamase


Mass: 31009.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue 1- 27 signal peptide / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-14, bla_2, SAMEA3512100_05103 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7BGE9, beta-lactamase
#2: Chemical ChemComp-WPP / Piperacillin / (2S,5R,6R)-6-{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}-3,3-dimethyl-7-oxo-4-thi a-1-azabicyclo[3.2.0]heptane-2-carboxylic acid


Mass: 517.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N5O7S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-YPP / Hydrolyzed piperacillin / (2R,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid


Mass: 535.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N5O8S / Feature type: SUBJECT OF INVESTIGATION
#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.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 4.5
Details: CTX-M-14 solution (22 mg/ml) was mixed with 45% precipitant solution (40% PEG8000, 200mM lithium sulfate, 100mM sodium acetate, pH 4.5) and with 5% undiluted seed stock in batch crystallization setups

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: environmental control box / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→78.07 Å / Num. obs: 27981 / % possible obs: 100 % / Redundancy: 45.2 % / Biso Wilson estimate: 26.44 Å2 / CC1/2: 0.862 / CC star: 0.962 / Net I/σ(I): 1.91
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 27.4 % / Mean I/σ(I) obs: 0.25 / Num. unique obs: 2739 / CC1/2: 0.034 / CC star: 0.257
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: Hare-Chip , silicon

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
CrystFEL0.10.2data reduction
CrystFEL0.10.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→78.07 Å / SU ML: 0.336 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.6164
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2556 1315 4.9 %
Rwork0.2281 25511 -
obs0.2295 26826 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.58 Å2
Refinement stepCycle: LAST / Resolution: 1.7→78.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 78 165 2184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182250
X-RAY DIFFRACTIONf_angle_d0.86133100
X-RAY DIFFRACTIONf_chiral_restr0.0467352
X-RAY DIFFRACTIONf_plane_restr0.0048416
X-RAY DIFFRACTIONf_dihedral_angle_d14.5165831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.47061030.4131948X-RAY DIFFRACTION67.22
1.77-1.850.41521500.40632800X-RAY DIFFRACTION98.53
1.85-1.950.42981370.34612894X-RAY DIFFRACTION99.64
1.95-2.070.30671540.28782883X-RAY DIFFRACTION99.93
2.07-2.230.26811590.27062914X-RAY DIFFRACTION99.93
2.23-2.450.28521350.24582939X-RAY DIFFRACTION99.87
2.45-2.810.28211590.23282957X-RAY DIFFRACTION100
2.81-3.530.21061620.20042971X-RAY DIFFRACTION99.97
3.54-78.070.20251560.17453205X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -4.62751831987 Å / Origin y: 1.41751536421 Å / Origin z: 19.8577705826 Å
111213212223313233
T0.242147323064 Å20.0549342682097 Å20.0120079236181 Å2-0.165080831853 Å20.0258068554837 Å2--0.143111355753 Å2
L0.761481285093 °20.0550813257003 °20.250894242009 °2-1.41494615363 °20.629212760723 °2--2.72097766536 °2
S0.00301826319317 Å °0.0259503347751 Å °0.0294445722559 Å °-0.212928592753 Å °-0.0217798130258 Å °0.0490140766929 Å °-0.403618038229 Å °-0.268175087326 Å °-0.00012520609253 Å °
Refinement TLS groupSelection details: all

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