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

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Basic information

Entry
Database: PDB / ID: 8isr
TitleCrystal structure of extended-spectrum class A beta-lactamase, CESS-1 E166Q acylated by cefaclor
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: 2.09 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 23, 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
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3248
Polymers57,3052
Non-polymers1,0206
Water9,026501
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2245
Polymers28,6521
Non-polymers5724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1003
Polymers28,6521
Non-polymers4482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.680, 70.410, 130.940
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

#1: Protein Beta-lactamase / CESS-1


Mass: 28652.281 Da / Num. of mol.: 2 / 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-Q6R / (R)-2-((R)-((R)-2-amino-2-phenylacetamido)(carboxy)methyl)-5-chloro-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / cefaclor


Mass: 385.823 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16ClN3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 288 K / Method: microbatch
Details: 0.1M 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: 2.09→30 Å / Num. obs: 34518 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 23.87 Å2 / CC1/2: 0.991 / Net I/σ(I): 7.4
Reflection shellResolution: 2.09→2.16 Å / Num. unique obs: 3187 / CC1/2: 0.66

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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: 2.09→29.774 Å / SU ML: 0.1953 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.6393
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2172 2000 5.8 %
Rwork0.1643 32507 -
obs0.1673 34507 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.81 Å2
Refinement stepCycle: LAST / Resolution: 2.09→29.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 64 503 4477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00674048
X-RAY DIFFRACTIONf_angle_d0.94035490
X-RAY DIFFRACTIONf_chiral_restr0.0529606
X-RAY DIFFRACTIONf_plane_restr0.0056734
X-RAY DIFFRACTIONf_dihedral_angle_d19.47811470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.24061400.19892289X-RAY DIFFRACTION100
2.14-2.20.2551420.2022300X-RAY DIFFRACTION100
2.2-2.260.28571400.19932274X-RAY DIFFRACTION100
2.26-2.340.24411400.1872287X-RAY DIFFRACTION100
2.34-2.420.25921410.182281X-RAY DIFFRACTION100
2.42-2.520.24821420.18012312X-RAY DIFFRACTION100
2.52-2.630.22911410.17572290X-RAY DIFFRACTION99.96
2.63-2.770.25971420.17152298X-RAY DIFFRACTION99.96
2.77-2.950.21251430.16372321X-RAY DIFFRACTION99.96
2.95-3.170.22481410.17252310X-RAY DIFFRACTION100
3.17-3.490.21451440.1592337X-RAY DIFFRACTION99.92
3.49-3.990.18611440.14672334X-RAY DIFFRACTION99.96
4-5.030.16981470.13032390X-RAY DIFFRACTION100
5.03-29.770.2051530.16312484X-RAY DIFFRACTION99.89

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