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- PDB-8iso: Crystal structure of extended-spectrum class A beta-lactamase, CESS-1 -

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Basic information

Entry
Database: PDB / ID: 8iso
TitleCrystal structure of extended-spectrum class A beta-lactamase, CESS-1
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
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Beta-lactamase
Similarity search - Component
Biological speciesStenotrophomonas sp. KCTC 12332 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsJeong, B.G. / Kim, M.Y. / Jeong, C.S. / Do, H.W. / Lee, J.H. / Cha, S.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Not funded Korea, Republic Of
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

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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)29,88719
Polymers28,6531
Non-polymers1,23318
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint30 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.580, 61.580, 149.490
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-637-

HOH

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Components

#1: Protein Beta-lactamase / CESS-1


Mass: 28653.266 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.54 Å3/Da / Density % sol: 51.67 %
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: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.29→30 Å / Num. obs: 73173 / % possible obs: 99.9 % / Redundancy: 25.1 % / Biso Wilson estimate: 14.13 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.27
Reflection shellResolution: 1.29→1.35 Å / Num. unique obs: 9146 / CC1/2: 0.893

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata scaling
Coot0.8.9model building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O7E

1o7e


Resolution: 1.29→28.47 Å / SU ML: 0.1126 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.2415 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1877 2000 2.73 %
Rwork0.1701 71169 -
obs0.1706 73169 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.15 Å2
Refinement stepCycle: LAST / Resolution: 1.29→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 80 241 2276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652095
X-RAY DIFFRACTIONf_angle_d0.96192810
X-RAY DIFFRACTIONf_chiral_restr0.0858304
X-RAY DIFFRACTIONf_plane_restr0.0066375
X-RAY DIFFRACTIONf_dihedral_angle_d14.31571207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.320.22161390.21584978X-RAY DIFFRACTION99.53
1.32-1.360.23671410.22124987X-RAY DIFFRACTION99.67
1.36-1.40.22931410.21065006X-RAY DIFFRACTION99.77
1.4-1.440.21471400.1974995X-RAY DIFFRACTION99.88
1.44-1.490.20661420.18535039X-RAY DIFFRACTION99.92
1.49-1.550.18821410.17775012X-RAY DIFFRACTION99.92
1.55-1.630.19561410.17945042X-RAY DIFFRACTION99.96
1.63-1.710.20491430.17345060X-RAY DIFFRACTION99.96
1.71-1.820.19521410.17085069X-RAY DIFFRACTION100
1.82-1.960.18471430.1635040X-RAY DIFFRACTION99.9
1.96-2.160.16831430.15875119X-RAY DIFFRACTION100
2.16-2.470.19761450.16055156X-RAY DIFFRACTION99.96
2.47-3.110.19881460.16525211X-RAY DIFFRACTION99.98
3.11-28.470.16551540.16625455X-RAY DIFFRACTION99.89

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