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- PDB-8r7m: CTX-M14 in complex with boric acid and 1,2-diol boric ester -

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Basic information

Entry
Database: PDB / ID: 8r7m
TitleCTX-M14 in complex with boric acid and 1,2-diol boric ester
ComponentsBeta-lactamase
KeywordsHYDROLASE / Lactamase
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
BORIC ACID / Chem-YCH / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsWerner, N. / Prester, A. / Hinrichs, W. / Perbandt, M. / Betzel, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research05K13GUA 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
DepositionNov 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 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

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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)28,6729
Polymers28,0011
Non-polymers6718
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-16 kcal/mol
Surface area11120 Å2
Unit cell
Length a, b, c (Å)41.775, 62.104, 86.508
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

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Protein , 1 types, 1 molecules A

#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) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S1JJX2, beta-lactamase

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Non-polymers , 6 types, 369 molecules

#2: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30 % PEG8000, 0.2 M lithium sulfate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1→37.62 Å / Num. obs: 120207 / % possible obs: 98.33 % / Redundancy: 17.2 % / Biso Wilson estimate: 8.73 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.058 / Net I/σ(I): 29.65
Reflection shellResolution: 1→1.06 Å / Mean I/σ(I) obs: 4.87 / Num. unique obs: 19343 / CC1/2: 0.904 / Rrim(I) all: 0.38

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→37.62 Å / SU ML: 0.0801 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.076
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1379 6009 5 %
Rwork0.1289 114198 -
obs0.1293 120207 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.85 Å2
Refinement stepCycle: LAST / Resolution: 1→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 41 361 2367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622143
X-RAY DIFFRACTIONf_angle_d1.01722935
X-RAY DIFFRACTIONf_chiral_restr0.0792344
X-RAY DIFFRACTIONf_plane_restr0.0111384
X-RAY DIFFRACTIONf_dihedral_angle_d6.9083331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.28781470.26382793X-RAY DIFFRACTION72.54
1.01-1.020.26291720.24413271X-RAY DIFFRACTION84.8
1.02-1.030.25491850.21713505X-RAY DIFFRACTION91.81
1.03-1.050.21051930.21173669X-RAY DIFFRACTION95.31
1.05-1.060.22891970.19443750X-RAY DIFFRACTION97.82
1.06-1.080.19212030.17563853X-RAY DIFFRACTION99.51
1.08-1.090.15462000.15633832X-RAY DIFFRACTION99.7
1.09-1.110.16222010.14273811X-RAY DIFFRACTION99.78
1.11-1.120.16582010.13313838X-RAY DIFFRACTION99.73
1.12-1.140.15142030.12653846X-RAY DIFFRACTION99.58
1.14-1.160.13092030.12573851X-RAY DIFFRACTION99.95
1.16-1.180.14132030.12353863X-RAY DIFFRACTION99.85
1.18-1.210.13382030.12593850X-RAY DIFFRACTION99.88
1.21-1.230.14792030.12333865X-RAY DIFFRACTION99.85
1.23-1.260.13342010.12533821X-RAY DIFFRACTION99.85
1.26-1.290.13832050.1193883X-RAY DIFFRACTION99.8
1.29-1.320.12692040.11683876X-RAY DIFFRACTION99.98
1.32-1.350.13232040.11463869X-RAY DIFFRACTION100
1.35-1.390.14872050.11233894X-RAY DIFFRACTION99.76
1.39-1.440.13892040.10983876X-RAY DIFFRACTION99.98
1.44-1.490.12342020.10873852X-RAY DIFFRACTION99.66
1.49-1.550.12712040.10483877X-RAY DIFFRACTION99.9
1.55-1.620.12642040.10923875X-RAY DIFFRACTION99.95
1.62-1.710.12522060.11013908X-RAY DIFFRACTION99.78
1.71-1.810.1212060.11643912X-RAY DIFFRACTION99.95
1.81-1.950.13012050.11373894X-RAY DIFFRACTION99.73
1.95-2.150.10582080.11023952X-RAY DIFFRACTION99.76
2.15-2.460.12952080.11543956X-RAY DIFFRACTION99.88
2.46-3.10.12522100.13223995X-RAY DIFFRACTION99.9
3.1-37.620.14242190.14724161X-RAY DIFFRACTION99.59

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