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

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Basic information

Entry
Database: PDB / ID: 8isp
TitleCrystal structure of extended-spectrum class A beta-lactamase, CESS-1 E166Q acylated by cephalexin
ComponentsBeta-lactamase
KeywordsHYDROLASE / extended-spectrum Class A beta-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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesStenotrophomonas sp. KCTC 12332 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 1.1Oct 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)29,0182
Polymers28,6521
Non-polymers3651
Water3,567198
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)62.118, 62.118, 150.448
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-455-

HOH

21A-588-

HOH

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Components

#1: Protein Beta-lactamase / CESS-1


Mass: 28652.281 Da / Num. of mol.: 1 / Mutation: E166Q
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-Q53 / (R)-2-((R)-((R)-2-amino-2-phenylacetamido)(carboxy)methyl)-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / cephalexin


Mass: 365.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
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 27, 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: 2.1→50 Å / Num. obs: 17064 / % possible obs: 95.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 24.16 Å2 / CC1/2: 0.98 / Net I/σ(I): 15.75
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 873 / CC1/2: 0.893

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data collection
Coot0.8.9model building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ISO

8iso


Resolution: 2.11→37.93 Å / SU ML: 0.2152 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 20.4368 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2431 1704 10 %
Rwork0.193 15336 -
obs0.1981 17040 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.82 Å2
Refinement stepCycle: LAST / Resolution: 2.11→37.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 24 199 2172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222013
X-RAY DIFFRACTIONf_angle_d0.6212733
X-RAY DIFFRACTIONf_chiral_restr0.0403302
X-RAY DIFFRACTIONf_plane_restr0.0036366
X-RAY DIFFRACTIONf_dihedral_angle_d6.60711195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.170.27831390.21871253X-RAY DIFFRACTION96
2.17-2.240.25871440.22341294X-RAY DIFFRACTION98.83
2.24-2.320.2771430.20471283X-RAY DIFFRACTION98.96
2.32-2.410.28961440.20571298X-RAY DIFFRACTION99.11
2.41-2.520.26831450.20481301X-RAY DIFFRACTION98.91
2.52-2.650.25791440.19511302X-RAY DIFFRACTION99.11
2.65-2.820.2431450.19131308X-RAY DIFFRACTION98.44
2.82-3.040.24871450.20341299X-RAY DIFFRACTION98.37
3.04-3.340.25531420.21011282X-RAY DIFFRACTION95.12
3.34-3.820.25821380.1891242X-RAY DIFFRACTION92.12
3.82-4.820.19761270.16531150X-RAY DIFFRACTION83.25
4.82-37.930.2071480.17751324X-RAY DIFFRACTION89.48

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