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- PDB-2xqz: Neutron structure of the perdeuterated Toho-1 R274N R276N double ... -

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Basic information

Entry
Database: PDB / ID: 2xqz
TitleNeutron structure of the perdeuterated Toho-1 R274N R276N double mutant beta-lactamase
ComponentsBETA-LACTAMSE TOHO-1
KeywordsHYDROLASE / EXTENDED-SPECTRUM BETA-LACTAMASES (ESBLS) / CTX-M-TYPE 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. / Wang, K.K. / Weiss, K.L. / Blakeley, M.P. / Cooper, J. / Chen, Y. / Coates, L.
CitationJournal: FEBS Lett. / Year: 2011
Title: The Active Site Protonation States of Perdeuterated Toho-1 Beta-Lactamase Determined by Neutron Diffraction Support a Role for Glu166 as the General Base in Acylation.
Authors: Tomanicek, S.J. / Wang, K.K. / Weiss, K.L. / Blakeley, M.P. / Cooper, J. / Chen, Y. / Coates, L.
History
DepositionSep 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 2.0Dec 27, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _pdbx_database_status.status_code_sf / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.pdbx_PDB_helix_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id
Revision 2.1Jan 31, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 2.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)27,9911
Polymers27,9911
Non-polymers00
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.956, 72.956, 98.526
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 BETA-LACTAMSE TOHO-1 / PERDEUTERATED TOHO-1 BETA-LACTAMASE


Mass: 27990.607 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-291 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FULLY PERDEUTERATED / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / 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.: 205 / Source method: isolated from a natural source / Formula: D2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 275 TO ASN ENGINEERED RESIDUE IN CHAIN A, ARG 277 TO ASN

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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

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.27 % / Description: 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: Jul 7, 2010
RadiationScattering type: neutron
Radiation wavelengthWavelength: 3.7 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.139
ReflectionResolution: 2.1→63.15 Å / Num. obs: 14991 / % possible obs: 83.7 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.18 / Rsym value: 0.06

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
LAUEGENdata reduction
LAUEGENdata scaling
RefinementResolution: 2.1→53.185 Å / σ(F): 1.55 / Phase error: 26.26 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2586 807 5.4 %
Rwork0.2246 --
obs0.2275 14990 82.29 %
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.95 Å2 / ksol: 0.522 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5001 Å2-0 Å20 Å2
2---2.5001 Å2-0 Å2
3---5.0001 Å2
Refinement stepCycle: LAST / Resolution: 2.1→53.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 0 205 2169
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0044110
NEUTRON DIFFRACTIONf_angle_d0.6677273
NEUTRON DIFFRACTIONf_dihedral_angle_d13.2281095
NEUTRON DIFFRACTIONf_chiral_restr0.042321
NEUTRON DIFFRACTIONf_plane_restr0.003628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1033-2.26560.29571060.23532070NEUTRON DIFFRACTION58
2.2656-2.49350.25061480.23242736NEUTRON DIFFRACTION77
2.4935-2.85410.30811570.2372947NEUTRON DIFFRACTION82
2.8541-3.59480.24361650.2283099NEUTRON DIFFRACTION86
3.5948-29.31870.24511770.2083350NEUTRON DIFFRACTION89

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