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

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Basic information

Entry
Database: PDB / ID: 8pcq
TitleStructure of serine-beta-lactamase CTX-M-14 following the time-resolved active site binding of boric acid and subsequent glycerol-boric acid-ester formation, 500 ms
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 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
BORATE ION / Chem-YCH / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)28,2934
Polymers28,0011
Non-polymers2933
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-21 kcal/mol
Surface area10520 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

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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-YCH / [(4~{S})-2-oxidanyl-1,3,2-dioxaborolan-4-yl]methanol


Mass: 117.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7BO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BO4 / BORATE ION


Mass: 78.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH4O4 / 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.: 235 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 293 K / Method: batch mode
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 EIGER2 X 16M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.52→38.88 Å / Num. obs: 38024 / % possible obs: 99.8 % / Redundancy: 3101 % / Biso Wilson estimate: 19.41 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 18.55
Reflection shellResolution: 1.52→1.54 Å / Num. unique obs: 2425 / CC1/2: 0.218 / CC star: 0.598
Serial crystallography sample deliveryDescription: CFEL TapeDrive / Method: injection

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→38.88 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7404
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1664 2078 5.81 %
Rwork0.1389 33706 -
obs0.1405 35784 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.8 Å2
Refinement stepCycle: LAST / Resolution: 1.55→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 17 235 2201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082100
X-RAY DIFFRACTIONf_angle_d1.06712879
X-RAY DIFFRACTIONf_chiral_restr0.0489338
X-RAY DIFFRACTIONf_plane_restr0.0072382
X-RAY DIFFRACTIONf_dihedral_angle_d13.325795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.39521360.35972182X-RAY DIFFRACTION99.36
1.59-1.630.30651370.29922169X-RAY DIFFRACTION99.83
1.63-1.670.27961320.24142222X-RAY DIFFRACTION99.62
1.67-1.720.22171340.19152183X-RAY DIFFRACTION99.74
1.72-1.770.19751340.16832203X-RAY DIFFRACTION99.87
1.77-1.840.17531410.14622210X-RAY DIFFRACTION99.75
1.84-1.910.18741350.13542261X-RAY DIFFRACTION99.92
1.91-20.15111370.12132195X-RAY DIFFRACTION99.87
2-2.10.15821340.11612238X-RAY DIFFRACTION99.87
2.1-2.240.14731360.11472214X-RAY DIFFRACTION100
2.24-2.410.16251400.11852265X-RAY DIFFRACTION99.92
2.41-2.650.14891420.13132267X-RAY DIFFRACTION99.96
2.65-3.030.17241440.13472291X-RAY DIFFRACTION100
3.03-3.820.14721420.11952341X-RAY DIFFRACTION99.96
3.82-38.880.14261540.12892465X-RAY DIFFRACTION99.43

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