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- PDB-2zq9: Cephalothin acyl-intermediate structure of class a beta-lactamase... -

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Basic information

Entry
Database: PDB / ID: 2zq9
TitleCephalothin acyl-intermediate structure of class a beta-lactamase Toho-1 E166A/R274N/R276N triple mutant
ComponentsBeta-lactamase Toho-1
KeywordsHYDROLASE / EXTENDED-SPECTRUM / ESBL / BETA-LACTAMASE / ACYL-ENZYME / COMPLEX / CEPHALOTHIN / TOHO-1 / Antibiotic resistance / Plasmid
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
Chem-CEO / CEPHALOTHIN / THIOPHENEACETIC ACID / Beta-lactamase Toho-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsNitanai, Y. / Shimamura, T. / Uchiyama, T. / Ishii, Y. / Takehira, M. / Yutani, K. / Matsuzawa, H. / Miyano, M.
CitationJournal: To be Published
Title: Structural Basis of Extend Spectrum Beta-Lactamase in Correlation of Enzymatic Kinetics and Thermal Stability of Acyl-Intermediates
Authors: Nitanai, Y. / Shimamura, T. / Uchiyama, T. / Ishii, Y. / Takehira, M. / Yutani, K. / Matsuzawa, H. / Miyano, M.
History
DepositionAug 7, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,1876
Polymers28,1181
Non-polymers1,0695
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.421, 72.421, 97.518
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase Toho-1


Mass: 28117.752 Da / Num. of mol.: 1 / Mutation: E166A, R274N, R276N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: PUC119 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q47066, beta-lactamase

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Non-polymers , 5 types, 358 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CEO / 5-METHYLENE-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-5,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID / HYDROLYZED CEPHALOTHIN


Mass: 338.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N2O4S2
#4: Chemical ChemComp-CLS / CEPHALOTHIN / 3-ACETOXYMETHYL-8-OXO-7-(2-THIOPHEN-2-YL-ACETYLAMINO)-5-THIA-1-AZA-BICYCLO[4.2.0]OCT-2-ENE-2-CARBOXYLIC ACID


Mass: 396.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N2O6S2
#5: Chemical ChemComp-SPA / THIOPHENEACETIC ACID


Mass: 142.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.95-2.10M ammonium sulfate, 0.2M sodium citrate, PH5.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 / Wavelength: 0.7 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 11, 2007 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.71
ReflectionResolution: 1.07→50 Å / Num. obs: 129204 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 47.01
Reflection shellResolution: 1.07→1.09 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.61 / % possible all: 91.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZQ7

2zq7


Resolution: 1.07→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.477 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.14625 6485 5 %RANDOM
Rwork0.13261 ---
obs0.13329 122579 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.414 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.07→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 75 395 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222211
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9993043
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2295304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70625.76192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55215383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5111511
X-RAY DIFFRACTIONr_chiral_restr0.090.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021665
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21137
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21543
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1191.51396
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68722229
X-RAY DIFFRACTIONr_scbond_it2.1363888
X-RAY DIFFRACTIONr_scangle_it3.094.5791
X-RAY DIFFRACTIONr_rigid_bond_restr1.05632284
X-RAY DIFFRACTIONr_sphericity_free4.6593397
X-RAY DIFFRACTIONr_sphericity_bonded3.72332154
LS refinement shellResolution: 1.07→1.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.16 405 -
Rwork0.145 8448 -
obs--92.05 %

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