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- PDB-2zq7: Apo structure of Class A beta-lactamase Toho-1 E166A/R274N/R276N ... -

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Basic information

Entry
Database: PDB / ID: 2zq7
TitleApo structure of Class A beta-lactamase Toho-1 E166A/R274N/R276N triple 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: 0.94 Å
AuthorsShimamura, T. / Nitanai, Y. / Uchiyama, T. / Ago, H. / Matsuzawa, H. / Miyano, M.
CitationJournal: To be Published
Title: Improvement of the Crystal Quality by the Surface Mutations on a Beta-Lactamase Toho-1
Authors: Shimamura, T. / Nitanai, Y. / Uchiyama, T. / Ago, H. / 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_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)28,5986
Polymers28,1181
Non-polymers4805
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.545, 72.545, 97.656
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

21A-413-

HOH

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Components

#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
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
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: Dec 10, 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: 0.94→50 Å / Num. obs: 192768 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 25.99
Reflection shellResolution: 0.94→0.96 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 4.32 / % possible all: 98.9

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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 1IYO

1iyo


Resolution: 0.94→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.346 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.14726 9670 5 %RANDOM
Rwork0.13519 ---
obs0.1358 182648 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.475 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.12 Å20 Å2
2---0.23 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 0.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 30 511 2808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222346
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9753221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3545325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84125.34103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69515417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0071514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021773
X-RAY DIFFRACTIONr_nbd_refined0.2070.21119
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21522
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2311
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.250
X-RAY DIFFRACTIONr_mcbond_it1.2851.51517
X-RAY DIFFRACTIONr_mcangle_it1.84722403
X-RAY DIFFRACTIONr_scbond_it2.3143915
X-RAY DIFFRACTIONr_scangle_it3.1594.5798
X-RAY DIFFRACTIONr_rigid_bond_restr1.04932432
X-RAY DIFFRACTIONr_sphericity_free5.023511
X-RAY DIFFRACTIONr_sphericity_bonded4.63432297
LS refinement shellResolution: 0.94→0.964 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.166 689 -
Rwork0.16 13286 -
obs--99.16 %

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