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- PDB-5kmw: TOHO1 Beta lactamase mutant E166A/R274N/R276N -benzyl penicillin ... -

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Basic information

Entry
Database: PDB / ID: 5kmw
TitleTOHO1 Beta lactamase mutant E166A/R274N/R276N -benzyl penicillin complex
ComponentsBeta-lactamase Toho-1
KeywordsHYDROLASE / Class A beta-lactamase / substrate recognition / acyl-enzyme
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
OPEN FORM - PENICILLIN G / PENICILLIN G / Beta-lactamase Toho-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsCoates, L. / Langan, P.S. / Vandavasi, V.G. / Weiss, K.L. / Cooper, J.B. / Ginell, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)32102548 United States
CitationJournal: to be published
Title: TOHO1 Beta lactamase mutant E166A/R274N/R276N -benzyl penicillin complex
Authors: Coates, L. / Langan, P.S. / Vandavasi, V.G. / Weiss, K.L. / Cooper, J.B. / Ginell, S.L.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.2Dec 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,9899
Polymers27,5031
Non-polymers1,4868
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.262, 72.262, 98.193
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-3078-

HOH

21A-3264-

HOH

31A-3337-

HOH

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Components

#1: Protein Beta-lactamase Toho-1


Mass: 27503.123 Da / Num. of mol.: 1 / Mutation: E165A, R271N, R273N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Production host: Escherichia coli (E. coli) / References: UniProt: Q47066, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G / Benzylpenicillin


Mass: 336.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O4S / Comment: antibiotic*YM
#4: Chemical ChemComp-PNN / PENICILLIN G / Benzylpenicillin


Mass: 334.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18N2O4S / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 293.15 K / Method: batch mode / pH: 6.1
Details: 30 microliters of 10 mg/ml protein concentration was added to a solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1). For ligand soaking, crystals were placed for 2-3 ...Details: 30 microliters of 10 mg/ml protein concentration was added to a solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1). For ligand soaking, crystals were placed for 2-3 h in a reservoir solution containing 2.7 M ammonium sulfate, 0.1 M sodium citrate (pH 6.1), and 5.0 mM benzyl penicillin. The crystals were then placed momentarily in a reservoir solution containing a cryoprotectant (30% w/v trehalose) and subsequently flash-frozen in liquid nitrogen

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Data collection

DiffractionMean temperature: 15 K
Ambient temp details: Cryo industries of America cryocool Helium cryostream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.67 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.67 Å / Relative weight: 1
ReflectionResolution: 1.1→38.62 Å / Num. obs: 118234 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.6
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 98.6

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Processing

Software
NameVersionClassification
SHELXL-97refinement
XDSBUILT=20160617data scaling
SCALA3.3.18data scaling
Coot0.83model building
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→10 Å / Num. parameters: 23165 / Num. restraintsaints: 28142 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
Rfactor% reflectionSelection details
Rfree0.17 -RANDOM
obs0.136 98.4 %-
Refine analyzeNum. disordered residues: 19 / Occupancy sum non hydrogen: 2443.8
Refinement stepCycle: 1 / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 94 516 2623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0147
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.005
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.4
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.0988
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0436
X-RAY DIFFRACTIONs_approx_iso_adps0.1587

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