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- PDB-1iyo: Toho-1 beta-Lactamase In Complex With Cefotaxime -

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Basic information

Entry
Database: PDB / ID: 1iyo
TitleToho-1 beta-Lactamase In Complex With Cefotaxime
ComponentsToho-1 beta-lactamase
KeywordsHYDROLASE / extended-spectrum / ESBL / BETA-LACTAMASE / ACYL-ENZYME / cefotaxime / complex
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 / 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 Toho-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShimamura, T. / Ibuka, A. / Fushinobu, S. / Wakagi, T. / Ishiguro, M. / Ishii, Y. / Matsuzawa, H.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Acyl-intermediate Structures of the Extended-spectrum Class A beta -Lactamase, Toho-1, in Complex with Cefotaxime, Cephalothin, and Benzylpenicillin.
Authors: Shimamura, T. / Ibuka, A. / Fushinobu, S. / Wakagi, T. / Ishiguro, M. / Ishii, Y. / Matsuzawa, H.
History
DepositionSep 4, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 15, 2017Group: Non-polymer description
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toho-1 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8905
Polymers28,2041
Non-polymers6864
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.581, 72.581, 98.179
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Toho-1 beta-lactamase


Mass: 28203.936 Da / Num. of mol.: 1 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pUC119 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47066, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7 / Details: Ibuka, A., (1999) J. Mol. Biol., 285, 2079.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.8 Mammonium sulfate1reservoir
2100 mMacetate1reservoirpH4.5-4.7
315 mg/mlprotein1drop
45 mMTris-HCl1droppH7.0

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 26985 / % possible obs: 95.2 % / Observed criterion σ(I): 0.1 / Rmerge(I) obs: 0.073
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 96844

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40 Å / σ(F): 3
RfactorNum. reflectionSelection details
Rfree0.206 -RANDOM
Rwork0.178 --
obs-26985 -
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 41 216 2224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.33

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