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- PDB-8isq: Crystal structure of extended-spectrum class A beta-lactamase, CE... -

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Basic information

Entry
Database: PDB / ID: 8isq
TitleCrystal structure of extended-spectrum class A beta-lactamase, CESS-1 E166Q acylated by ampicillin
ComponentsBeta-lactamase
KeywordsHYDROLASE / extended-spectrum Class A beta-lactamase
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-ZZ7 / Beta-lactamase
Similarity search - Component
Biological speciesStenotrophomonas sp. KCTC 12332 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsJeong, B.G. / Kim, M.Y. / Jeong, C.S. / Do, H.W. / Lee, J.H. / Cha, S.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Antimicrob Agents / Year: 2024
Title: Characterization of the extended substrate spectrum of the class A beta-lactamase CESS-1 from Stenotrophomonas sp. and structure-based investigation into its substrate preference.
Authors: Jeong, B.G. / Kim, M.Y. / Jeong, C.S. / Do, H. / Hwang, J. / Lee, J.H. / Cha, S.S.
History
DepositionMar 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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)29,3214
Polymers28,6521
Non-polymers6693
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.350, 61.350, 140.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-473-

HOH

21A-544-

HOH

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Components

#1: Protein Beta-lactamase / CESS-1


Mass: 28652.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas sp. KCTC 12332 (bacteria)
Gene: AXG53_04720 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A126NGE0, beta-lactamase
#2: Chemical ChemComp-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 367.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 288 K / Method: microbatch
Details: 0.1 M Bis-Tris pH 6.5, 20% (w/v) polyethylene glycol (PEG) monomethyl ether (MME) 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 26, 2022
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.24→30 Å / Num. obs: 13572 / % possible obs: 99.9 % / Redundancy: 25.1 % / Biso Wilson estimate: 33.69 Å2 / CC1/2: 0.995 / Net I/σ(I): 8.82
Reflection shellResolution: 2.24→2.31 Å / Num. unique obs: 1167 / CC1/2: 0.736

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata scaling
Coot0.8.9model building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ISO

8iso


Resolution: 2.24→28.104 Å / SU ML: 0.249 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2241 1358 10.01 %
Rwork0.1697 12208 -
obs0.1752 13566 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.81 Å2
Refinement stepCycle: LAST / Resolution: 2.24→28.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 44 145 2151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682043
X-RAY DIFFRACTIONf_angle_d0.99012774
X-RAY DIFFRACTIONf_chiral_restr0.0494306
X-RAY DIFFRACTIONf_plane_restr0.0059368
X-RAY DIFFRACTIONf_dihedral_angle_d17.4933756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.320.30751330.22911189X-RAY DIFFRACTION100
2.32-2.410.33041320.22911193X-RAY DIFFRACTION99.77
2.41-2.520.24121320.19961184X-RAY DIFFRACTION99.92
2.52-2.660.28071330.19271200X-RAY DIFFRACTION100
2.66-2.820.27291330.18741200X-RAY DIFFRACTION99.85
2.82-3.040.26811340.19651201X-RAY DIFFRACTION100
3.04-3.340.27041350.1921223X-RAY DIFFRACTION100
3.34-3.830.18521370.16291229X-RAY DIFFRACTION99.93
3.83-4.820.2011390.12911248X-RAY DIFFRACTION100
4.82-28.10.16061500.1461341X-RAY DIFFRACTION100

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