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- PDB-2wyx: Neutron structure of a class A Beta-lactamase Toho-1 E166A R274N ... -

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Basic information

Entry
Database: PDB / ID: 2wyx
TitleNeutron structure of a class A Beta-lactamase Toho-1 E166A R274N R276N triple mutant
ComponentsBETA-LACTAMSE TOHO-1
KeywordsHYDROLASE / TOHO-1 / BETA-LACTAMASE / CTX- M-TYPE ESBLS / NEUTRON STRUCTURE / ANTIBIOTIC RESISTANCE / EXTENDED-SPECTRUM BETA-LACTAMASES (ESBLS)
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
DEUTERATED WATER / Beta-lactamase Toho-1
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 2.1 Å
AuthorsTomanicek, S.J. / Blakeley, M.P. / Cooper, J. / Chen, Y. / Afonine, P. / Coates, L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Neutron Diffraction Studies of a Class a Beta-Lactamase Toho-1 E166A R274N R276N Triple Mutant
Authors: Tomanicek, S.J. / Blakeley, M.P. / Cooper, J. / Chen, Y. / Afonine, P. / Coates, L.
History
DepositionNov 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 1.2May 9, 2018Group: Data collection / Category: diffrn_source / reflns / reflns_shell
Item: _diffrn_source.pdbx_synchrotron_beamline / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMSE TOHO-1


Theoretical massNumber of molelcules
Total (without water)27,5031
Polymers27,5031
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.993, 72.993, 98.365
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-2193-

HOH

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Components

#1: Protein BETA-LACTAMSE TOHO-1


Mass: 27503.123 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-288 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21 / Description: RECOMBINANT / Plasmid: PJEXPRESS401 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q47066, beta-lactamase
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: D2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 169 TO ALA ENGINEERED RESIDUE IN CHAIN A, ARG 275 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, GLU 169 TO ALA ENGINEERED RESIDUE IN CHAIN A, ARG 275 TO ASN ENGINEERED RESIDUE IN CHAIN A, ARG 277 TO ASN
Sequence detailsRESIDUES 29-287 PRESENT IN THIS NEUTRON STRUCTURE.

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDescription: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

Diffraction sourceSource: NUCLEAR REACTOR / Site: ILL / Beamline: LADI III / Wavelength: 3.7 / Wavelength: 3.7 Å
DetectorDetector: IMAGE PLATE / Date: Sep 3, 2009
RadiationScattering type: neutron
Radiation wavelengthWavelength: 3.7 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.201
ReflectionResolution: 2.1→19.4 Å / Num. obs: 15814 / % possible obs: 88.6 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Rmerge(I) obs: 0.177 / Rsym value: 0.06 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 7 / % possible all: 78

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
LAUEGENdata reduction
LAUEGENdata scaling
RefinementResolution: 2.1→19.409 Å / σ(F): 1.52 / Phase error: 30.31 / Stereochemistry target values: MLF
RfactorNum. reflection% reflection
Rfree0.2579 840 5.3 %
Rwork0.2229 --
obs0.226 15814 88.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.627 Å2 / ksol: 0.477 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9814 Å20 Å20 Å2
2---0.9814 Å2-0 Å2
3---1.9627 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 0 160 2085
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0144508
NEUTRON DIFFRACTIONf_angle_d1.17937
NEUTRON DIFFRACTIONf_dihedral_angle_d19.251100
NEUTRON DIFFRACTIONf_chiral_restr0.083318
NEUTRON DIFFRACTIONf_plane_restr0.004903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.102-2.26390.29441300.26042621NEUTRON DIFFRACTION74
2.2639-2.49090.30031440.2532787NEUTRON DIFFRACTION78
2.4909-2.84960.26881550.22922974NEUTRON DIFFRACTION83
2.8496-3.58350.25531700.20783211NEUTRON DIFFRACTION89
3.5835-16.00120.22751850.20483388NEUTRON DIFFRACTION90

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