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- PDB-9g7y: CTX-M-14 apo serial crystallography temperature series; 40C, 313K -

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Basic information

Entry
Database: PDB / ID: 9g7y
TitleCTX-M-14 apo serial crystallography temperature series; 40C, 313K
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
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)31,1052
Polymers31,0091
Non-polymers961
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-17 kcal/mol
Surface area10540 Å2
Unit cell
Length a, b, c (Å)41.850, 41.850, 232.850
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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.9 Å3/Da / Density % sol: 35.2 %
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: 313 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: Feb 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→77.62 Å / Num. obs: 27454 / % possible obs: 100 % / Redundancy: 333.9 % / Biso Wilson estimate: 23.14 Å2 / CC1/2: 0.978 / CC star: 0.994 / R split: 0.112 / Net I/σ(I): 7.02
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 202.7 % / Mean I/σ(I) obs: 1.71 / Num. unique obs: 2685 / CC1/2: 0.714 / CC star: 0.913 / R split: 0.59 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: Hare-Chip , silicon
Serial crystallography data reductionCrystal hits: 28818

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFEL0.10.2data reduction
CrystFEL0.10.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→77.62 Å / SU ML: 0.2199 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1784 1354 4.95 %
Rwork0.155 25989 -
obs0.1561 27343 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.2 Å2
Refinement stepCycle: LAST / Resolution: 1.7→77.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 5 147 2093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552092
X-RAY DIFFRACTIONf_angle_d0.82482872
X-RAY DIFFRACTIONf_chiral_restr0.0489339
X-RAY DIFFRACTIONf_plane_restr0.007383
X-RAY DIFFRACTIONf_dihedral_angle_d12.5845783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.27581120.25272563X-RAY DIFFRACTION99.74
1.76-1.830.28961230.25412548X-RAY DIFFRACTION99.89
1.83-1.910.2571600.18582523X-RAY DIFFRACTION99.78
1.91-2.020.1751160.14632561X-RAY DIFFRACTION99.93
2.02-2.140.16941670.14852505X-RAY DIFFRACTION100
2.14-2.310.17951050.14792622X-RAY DIFFRACTION99.96
2.31-2.540.18871470.15882549X-RAY DIFFRACTION100
2.54-2.910.17781320.16292629X-RAY DIFFRACTION99.96
2.91-3.660.1811470.1522645X-RAY DIFFRACTION100
3.66-77.620.1451450.13422844X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -5.53074039459 Å / Origin y: 1.54513009261 Å / Origin z: 19.6174633358 Å
111213212223313233
T0.185692471565 Å20.0373936052941 Å20.000252126965566 Å2-0.143833329233 Å20.0184648639392 Å2--0.166623815777 Å2
L0.644836766122 °20.112829152639 °20.0774526269395 °2-1.16447423355 °20.551647981222 °2--2.1120162373 °2
S0.020903281329 Å °0.0310933738638 Å °0.0143591831935 Å °-0.172115058864 Å °-0.000641335196271 Å °0.000976335638528 Å °-0.239574447993 Å °-0.179920251441 Å °0.000708193207869 Å °
Refinement TLS groupSelection details: all

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