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- PDB-2zq8: Apo structure of class a beta-lactamase Toho-1 R274N/R276N double... -

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Basic information

Entry
Database: PDB / ID: 2zq8
TitleApo structure of class a beta-lactamase Toho-1 R274N/R276N double mutant
ComponentsBeta-lactamase Toho-1
KeywordsHYDROLASE / EXTENDED-SPECTRUM / ESBL / BETA-LACTAMASE / 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
Beta-lactamase Toho-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsShimamura, T. / Nitanai, Y. / Uchiyama, T. / Ago, H. / Matsuzawa, H. / Miyano, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Improvement of crystal quality by surface mutations of beta-lactamase Toho-1
Authors: Shimamura, T. / Nitanai, Y. / Uchiyama, T. / Matsuzawa, H.
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 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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_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

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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)28,6566
Polymers28,1761
Non-polymers4805
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.511, 72.511, 97.477
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-291-

HOH

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Components

#1: Protein Beta-lactamase Toho-1


Mass: 28175.787 Da / Num. of mol.: 1 / Mutation: 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
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
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: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 21, 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
20.81
ReflectionResolution: 1.03→50 Å / Num. obs: 146345 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 27.17
Reflection shellResolution: 1.03→1.05 Å / Redundancy: 9 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 7.33 / % possible all: 99.9

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Processing

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

2zq7


Resolution: 1.03→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.459 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1481 7323 5 %RANDOM
Rwork0.13763 ---
obs0.13814 138865 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.223 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.09 Å20 Å2
2---0.19 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.03→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 30 455 2733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222323
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9773185
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2475319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43625.437103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13215415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2291514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021757
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21099
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21511
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1831.51498
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7422378
X-RAY DIFFRACTIONr_scbond_it2.2213902
X-RAY DIFFRACTIONr_scangle_it3.0964.5790
X-RAY DIFFRACTIONr_rigid_bond_restr1.07532400
X-RAY DIFFRACTIONr_sphericity_free4.5973455
X-RAY DIFFRACTIONr_sphericity_bonded4.22832278
LS refinement shellResolution: 1.03→1.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.137 548 -
Rwork0.125 10142 -
obs--99.8 %

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