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- PDB-7k2w: Crystal structure of CTX-M-14 E166A/K234R Beta-lactamase in compl... -

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Basic information

Entry
Database: PDB / ID: 7k2w
TitleCrystal structure of CTX-M-14 E166A/K234R Beta-lactamase in complex with hydrolyzed cefotaxime
ComponentsBeta-lactamase
KeywordsHYDROLASE / antibiotic resistance / acyl-enzyme intermediate
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CEFOTAXIME, C3' cleaved, open, bound form / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLu, S. / Palzkill, T. / Sankaran, B. / Hu, L. / Soeung, V. / Prasad, B.V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32956 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A drug-resistant beta-lactamase variant changes the conformation of its active-site proton shuttle to alter substrate specificity and inhibitor potency.
Authors: Soeung, V. / Lu, S. / Hu, L. / Judge, A. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
History
DepositionSep 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 1.3Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 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)28,0832
Polymers27,6851
Non-polymers3971
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.654, 41.654, 232.309
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-709-

HOH

21A-771-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 27685.184 Da / Num. of mol.: 1 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A2H4FY00, UniProt: Q9L5C7*PLUS, beta-lactamase
#2: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium Chloride 0.1 M Tris pH8 20%(w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.4→34.45 Å / Num. obs: 46585 / % possible obs: 98.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 9.97 Å2 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.012 / Net I/σ(I): 35.1
Reflection shellResolution: 1.4→3.6 Å / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 15.7 / Num. unique obs: 46589 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.4→34.45 Å / SU ML: 0.1632 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.3222
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2439 2321 4.98 %
Rwork0.1986 44264 -
obs0.2008 46585 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.67 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 26 380 2342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441991
X-RAY DIFFRACTIONf_angle_d0.82972710
X-RAY DIFFRACTIONf_chiral_restr0.0686320
X-RAY DIFFRACTIONf_plane_restr0.0072357
X-RAY DIFFRACTIONf_dihedral_angle_d18.5836300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.25481540.2282602X-RAY DIFFRACTION99.86
1.43-1.460.28341210.22972597X-RAY DIFFRACTION99.82
1.46-1.490.26241270.22952637X-RAY DIFFRACTION99.64
1.49-1.530.28871690.22592575X-RAY DIFFRACTION99.67
1.53-1.570.27881320.21882602X-RAY DIFFRACTION99.53
1.57-1.620.2481250.22082624X-RAY DIFFRACTION99.35
1.62-1.670.27081350.22052629X-RAY DIFFRACTION99.28
1.67-1.730.26161400.21092614X-RAY DIFFRACTION99.14
1.73-1.80.23961200.21022634X-RAY DIFFRACTION98.85
1.8-1.880.23191590.20992546X-RAY DIFFRACTION98.69
1.88-1.980.28341390.20392634X-RAY DIFFRACTION98.44
1.98-2.10.28071330.19832607X-RAY DIFFRACTION98.21
2.11-2.270.24451310.18812613X-RAY DIFFRACTION97.76
2.27-2.50.23811480.20012606X-RAY DIFFRACTION97.21
2.5-2.860.2121430.19592617X-RAY DIFFRACTION96.54
2.86-3.60.22091260.1772619X-RAY DIFFRACTION94.39
3.6-34.450.22211190.17852508X-RAY DIFFRACTION84.74

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