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- PDB-5ksc: E166A/R274N/R276N Toho-1 Beta-lactamase aztreonam acyl-enzyme int... -

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Basic information

Entry
Database: PDB / ID: 5ksc
TitleE166A/R274N/R276N Toho-1 Beta-lactamase aztreonam acyl-enzyme intermediate
ComponentsBeta-lactamase Toho-1
KeywordsHYDROLASE / Beta-lactamase / aztreonam / acyl-intermediate
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
Chem-AZR / DEUTERATED WATER / Beta-lactamase Toho-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVandavasi, V.G. / Langan, P.S. / Weiss, K. / Parks, J.M. / Cooper, J.B. / Ginell, S.L. / Coates, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)32102548 United States
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Active-Site Protonation States in an Acyl-Enzyme Intermediate of a Class A beta-Lactamase with a Monobactam Substrate.
Authors: Vandavasi, V.G. / Langan, P.S. / Weiss, K.L. / Parks, J.M. / Cooper, J.B. / Ginell, S.L. / Coates, L.
History
DepositionJul 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 6, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase Toho-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4842
Polymers28,0471
Non-polymers4371
Water52229
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.296, 73.296, 99.093
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-lactamase Toho-1


Mass: 28046.678 Da / Num. of mol.: 1 / Mutation: E169A, R275N, R277N
Source method: isolated from a genetically manipulated source
Details: Aztreonam / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Production host: Escherichia coli (E. coli) / References: UniProt: Q47066, beta-lactamase
#2: Chemical ChemComp-AZR / 2-({[(1Z)-1-(2-amino-1,3-thiazol-4-yl)-2-oxo-2-{[(2S,3S)-1-oxo-3-(sulfoamino)butan-2-yl]amino}ethylidene]amino}oxy)-2-methylpropanoic acid / AZTREONAM, open form / Aztreonam


Mass: 437.449 Da / Num. of mol.: 1 / Mutation: E169A, R275N, R277N
Source method: isolated from a genetically manipulated source
Formula: C13H19N5O8S2 / Details: Aztreonam / References: beta-lactamase / Comment: antibiotic*YM
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: D2O

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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: 1.97 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293.15 K / Method: batch mode / pH: 6.1
Details: 300 microliters of a 10 mg/ml protein concentration in a solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1) prepared in D2O.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: NUCLEAR REACTOR / Type: ORNL Spallation Neutron Source BEAMLINE MANDI / Wavelength: 2-4
DetectorType: ORNL ANGER CAMERA / Detector: AREA DETECTOR / Date: Mar 3, 2015
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
ReflectionResolution: 2.1→14.73 Å / Num. obs: 13173 / % possible obs: 71.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.2 / % possible all: 50.1

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Processing

Software
NameVersionClassification
Mantiddata processing
SHELXSHELXL-97refinement
SHELXphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→10 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 -5 %RANDOM
Rwork0.24 ---
obs-13173 72.1 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2024 / Occupancy sum non hydrogen: 2011.8
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 105 0 2071
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONs_bond_d0.0074
NEUTRON DIFFRACTIONs_angle_d
NEUTRON DIFFRACTIONs_similar_dist
NEUTRON DIFFRACTIONs_from_restr_planes0
NEUTRON DIFFRACTIONs_zero_chiral_vol
NEUTRON DIFFRACTIONs_non_zero_chiral_vol
NEUTRON DIFFRACTIONs_anti_bump_dis_restr
NEUTRON DIFFRACTIONs_rigid_bond_adp_cmpnt
NEUTRON DIFFRACTIONs_similar_adp_cmpnt
NEUTRON DIFFRACTIONs_approx_iso_adps

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