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- PDB-8pc9: Structure of serine-beta-lactamase CTX-M-14 following the time-re... -

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Basic information

Entry
Database: PDB / ID: 8pc9
TitleStructure of serine-beta-lactamase CTX-M-14 following the time-resolved active site binding of boric acid, 0 ms - native.
ComponentsBeta-lactamase
KeywordsHYDROLASE / catalytic activity / beta-lactamase activity / hydrolase activity / inhibitor / time-resolved / tape drive
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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: 1.4 Å
AuthorsPrester, A. / Perbandt, M. / Galchenkova, M. / Oberthuer, D. / Yefanov, O. / Hinrichs, W. / Rohde, H. / Betzel, C.
Funding support Germany, 3items
OrganizationGrant numberCountry
Joachim Herz Stiftung Germany
German Federal Ministry for Education and Research Germany
German Research Foundation (DFG) Germany
CitationJournal: Commun Chem / Year: 2024
Title: Time-resolved crystallography of boric acid binding to the active site serine of the beta-lactamase CTX-M-14 and subsequent 1,2-diol esterification.
Authors: Prester, A. / Perbandt, M. / Galchenkova, M. / Oberthuer, D. / Werner, N. / Henkel, A. / Maracke, J. / Yefanov, O. / Hakanpaa, J. / Pompidor, G. / Meyer, J. / Chapman, H. / Aepfelbacher, M. ...Authors: Prester, A. / Perbandt, M. / Galchenkova, M. / Oberthuer, D. / Werner, N. / Henkel, A. / Maracke, J. / Yefanov, O. / Hakanpaa, J. / Pompidor, G. / Meyer, J. / Chapman, H. / Aepfelbacher, M. / Hinrichs, W. / Rohde, H. / Betzel, C.
History
DepositionJun 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0972
Polymers28,0011
Non-polymers961
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-16 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.840, 41.840, 233.280
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
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 28000.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ctx-m-14 / Production host: Escherichia coli (E. coli) / References: UniProt: D2D9A0, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 4.5
Details: 50% 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: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.4→17.77 Å / Num. obs: 48378 / % possible obs: 100 % / Redundancy: 2214 % / Biso Wilson estimate: 23.6 Å2 / CC1/2: 0.991 / CC star: 0.998 / Net I/σ(I): 9.09
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 3119 / CC1/2: 0.273 / CC star: 0.655
Serial crystallography sample deliveryDescription: CFEL TapeDrive / Method: injection

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot1.18.2_3874model building
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→17.64 Å / SU ML: 0.2135 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.7993
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1702 2791 5.81 %
Rwork0.1446 45231 -
obs0.1461 48022 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.37 Å2
Refinement stepCycle: LAST / Resolution: 1.4→17.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 5 235 2189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882095
X-RAY DIFFRACTIONf_angle_d0.97212873
X-RAY DIFFRACTIONf_chiral_restr0.0716338
X-RAY DIFFRACTIONf_plane_restr0.0091381
X-RAY DIFFRACTIONf_dihedral_angle_d12.9911788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.39331380.41632157X-RAY DIFFRACTION97.95
1.42-1.450.41941330.40472212X-RAY DIFFRACTION98.08
1.45-1.480.37811390.34212174X-RAY DIFFRACTION98.55
1.48-1.510.30291370.30922212X-RAY DIFFRACTION99.03
1.51-1.540.32551390.28512233X-RAY DIFFRACTION99.25
1.54-1.580.28411320.25052207X-RAY DIFFRACTION99.45
1.58-1.620.27211390.23972230X-RAY DIFFRACTION99.62
1.62-1.660.21851340.22062223X-RAY DIFFRACTION99.37
1.66-1.710.2411350.20332221X-RAY DIFFRACTION99.45
1.71-1.760.23661360.19732240X-RAY DIFFRACTION99.66
1.76-1.830.20261460.16012277X-RAY DIFFRACTION99.75
1.83-1.90.15821370.14592268X-RAY DIFFRACTION99.92
1.9-1.990.16611370.12352255X-RAY DIFFRACTION99.92
1.99-2.090.15341380.12592278X-RAY DIFFRACTION100
2.09-2.220.15541390.11912248X-RAY DIFFRACTION99.92
2.22-2.390.14271400.12082272X-RAY DIFFRACTION99.96
2.39-2.630.15071460.13362334X-RAY DIFFRACTION99.92
2.63-3.010.17221460.13512318X-RAY DIFFRACTION99.92
3.01-3.790.15471440.12232371X-RAY DIFFRACTION99.88
3.79-17.640.1431560.1272501X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: -4.20777344121 Å / Origin y: -3.93693022382 Å / Origin z: -19.162641364 Å
111213212223313233
T0.119849644602 Å2-0.00275680674784 Å2-0.0180020210939 Å2-0.238886667359 Å20.0178365270047 Å2--0.161709749811 Å2
L1.39258998205 °2-0.410757996701 °2-0.751194633445 °2-1.18597851802 °20.746081643577 °2--3.29780749893 °2
S0.0708654426638 Å °0.183752720406 Å °0.0238711342128 Å °-0.0592291475318 Å °-0.0699793691548 Å °0.0501497692026 Å °0.0107899703447 Å °-0.468004251038 Å °-0.0217764692657 Å °
Refinement TLS groupSelection details: all

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