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- PDB-8r37: Klebsiella pneumoniae fosfomycin-resistance protein (FosAKP) -

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Basic information

Entry
Database: PDB / ID: 8r37
TitleKlebsiella pneumoniae fosfomycin-resistance protein (FosAKP)
ComponentsFosA family fosfomycin resistance glutathione transferase
KeywordsTRANSFERASE / Antibiotic resistance / Klebsiella pneumoniae / Glutathione / Fosfomycin / metalloenzyme / biosensor
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / metal ion binding
Similarity search - Function
: / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Similarity search - Domain/homology
FOSFOMYCIN / : / : / L(+)-TARTARIC ACID / FosA family fosfomycin resistance glutathione transferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsPapageorgiou, A.C. / Varotsou, C. / Labrou, N.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Studies of Klebsiella pneumoniae Fosfomycin-Resistance Protein and Its Application for the Development of an Optical Biosensor for Fosfomycin Determination.
Authors: Varotsou, C. / Ataya, F. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionNov 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: FosA family fosfomycin resistance glutathione transferase
A: FosA family fosfomycin resistance glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,69718
Polymers32,9912
Non-polymers70616
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.620, 47.030, 149.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein FosA family fosfomycin resistance glutathione transferase


Mass: 16495.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The last eight C-terminal residues are flexible and not modelled.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: fosA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A086IRG1

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Non-polymers , 6 types, 398 molecules

#2: Chemical ChemComp-FCN / FOSFOMYCIN / 1,2-EPOXYPROPYLPHOSPHONIC ACID


Mass: 138.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O4P / Comment: antibiotic*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: PEG3350 18% w/v, potassium sodium tartrate 0.2 M, MnCl2 6 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.48→149.2 Å / Num. obs: 48410 / % possible obs: 99.4 % / Redundancy: 9.8 % / Biso Wilson estimate: 21.01 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.089 / Net I/σ(I): 11.8
Reflection shellResolution: 1.48→1.51 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2174 / CC1/2: 0.666 / Rrim(I) all: 1.452 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→44.85 Å / SU ML: 0.1838 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4427
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2057 2304 4.78 %
Rwork0.1731 45939 -
obs0.1746 48243 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.59 Å2
Refinement stepCycle: LAST / Resolution: 1.48→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 32 382 2594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552285
X-RAY DIFFRACTIONf_angle_d0.91163113
X-RAY DIFFRACTIONf_chiral_restr0.0845333
X-RAY DIFFRACTIONf_plane_restr0.0073404
X-RAY DIFFRACTIONf_dihedral_angle_d9.4323315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.510.35331330.34282615X-RAY DIFFRACTION91.75
1.51-1.550.33321370.30892755X-RAY DIFFRACTION97.64
1.55-1.590.28661400.25662799X-RAY DIFFRACTION98.46
1.59-1.630.25071370.23252889X-RAY DIFFRACTION99.7
1.63-1.680.24291430.2172850X-RAY DIFFRACTION99.77
1.68-1.730.24991420.21132830X-RAY DIFFRACTION99.8
1.73-1.790.23151450.19762862X-RAY DIFFRACTION99.77
1.79-1.860.24871130.19392899X-RAY DIFFRACTION99.87
1.86-1.950.21621450.17282872X-RAY DIFFRACTION99.8
1.95-2.050.21811760.17592855X-RAY DIFFRACTION99.9
2.05-2.180.21211460.16792876X-RAY DIFFRACTION99.9
2.18-2.350.21271460.17522898X-RAY DIFFRACTION99.93
2.35-2.590.21821440.17992912X-RAY DIFFRACTION99.93
2.59-2.960.20521620.18252929X-RAY DIFFRACTION99.97
2.96-3.730.18611490.14972962X-RAY DIFFRACTION99.97
3.73-44.850.16941460.14813136X-RAY DIFFRACTION99.88

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