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- PDB-4bd1: Neutron structure of a perdeuterated Toho-1 R274N R276N double mu... -

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Basic information

Entry
Database: PDB / ID: 4bd1
TitleNeutron structure of a perdeuterated Toho-1 R274N R276N double mutant Beta-lactamase in complex with a fully deuterated boronic acid (BZB)
ComponentsTOHO-1 BETA-LACTAMASE
KeywordsHYDROLASE / PERDEUTERATED NEUTRON STRUCTURE / EXTENDED-SPECTRUM BETA LACTAMASES / 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
BENZO[B]THIOPHENE-2-BORONIC ACID / DEUTERATED WATER / Beta-lactamase Toho-1
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 2.002 Å
AuthorsTomanicek, S.J. / Weiss, K.L. / Standaert, R.F. / Ostermann, A. / Schrader, T.E. / Ng, J.D. / Coates, L.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Neutron and X-Ray Crystal Structures of a Perdeuterated Enzyme Inhibitor Complex Reveal the Catalytic Proton Network of the Toho-1 Beta-Lactamase for the Acylation Reaction.
Authors: Tomanicek, S.J. / Standaert, R.F. / Weiss, K.L. / Ostermann, A. / Schrader, T.E. / Ng, J.D. / Coates, L.
History
DepositionOct 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Mar 22, 2017Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TOHO-1 BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2832
Polymers28,1051
Non-polymers1781
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.429, 73.429, 99.112
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-2016-

DOD

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Components

#1: Protein TOHO-1 BETA-LACTAMASE


Mass: 28104.713 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PERDEUTERATED / Source: (gene. exp.) ESCHERICHIA COLI BL21 (bacteria) / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: Q47066, beta-lactamase
#2: Chemical ChemComp-BZB / BENZO[B]THIOPHENE-2-BORONIC ACID


Mass: 178.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7BO2S
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: D2O
Nonpolymer detailsBENZO[B]THIOPHENE-2-BORONIC ACID (BZB): PERDEUTERATED

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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: 2.59 Å3/Da / Density % sol: 54.12 % / Description: NONE
Crystal growpH: 6.5 / Details: PH 6.5

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Data collection

Diffraction sourceSource: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 2.4
DetectorDate: Aug 8, 2012
RadiationScattering type: neutron
Radiation wavelengthWavelength: 2.4 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19436 / % possible obs: 90.2 % / Observed criterion σ(I): 3.7 / Redundancy: 4 % / Rmerge(I) obs: 0.15 / Rsym value: 0.08

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: NONE

Resolution: 2.002→9.974 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 961 5.1 %
Rwork0.2195 --
obs0.2214 18840 89.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 2 Å2 / ksol: 2 e/Å3
Refinement stepCycle: LAST / Resolution: 2.002→9.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 12 145 2127
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0194252
NEUTRON DIFFRACTIONf_angle_d1.1547375
NEUTRON DIFFRACTIONf_dihedral_angle_d13.7231102
NEUTRON DIFFRACTIONf_chiral_restr0.1322
NEUTRON DIFFRACTIONf_plane_restr0.008633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0023-2.10690.29771240.23182236NEUTRON DIFFRACTION79
2.1069-2.23750.24441410.19842272NEUTRON DIFFRACTION81
2.2375-2.4080.21211330.20272329NEUTRON DIFFRACTION83
2.408-2.64620.26091390.21282559NEUTRON DIFFRACTION90
2.6462-3.01980.27931450.22682710NEUTRON DIFFRACTION95
3.0198-3.77020.26541430.23272830NEUTRON DIFFRACTION98
3.7702-9.97450.25161360.22342943NEUTRON DIFFRACTION98

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