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- PDB-9e48: Crystal Structure of FosA from Pseudomonas aeruginosa with Mangan... -

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Basic information

Entry
Database: PDB / ID: 9.0E+48
TitleCrystal Structure of FosA from Pseudomonas aeruginosa with Manganese and Fosfomycin
ComponentsGlutathione transferase FosA
KeywordsTRANSFERASE / homodimer / fosfomycin resistance / antimicrobial resistance
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / response to antibiotic / metal ion binding / cytoplasm
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 / : / : / Glutathione transferase FosA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWiltsie, V. / Thompson, M.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM148956 United States
CitationJournal: To Be Published
Title: Crystal Structure of FosA from Pseudomonas aeruginosa with Manganese and Fosfomycin
Authors: Wiltsie, V. / Thompson, M.K.
History
DepositionOct 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione transferase FosA
B: Glutathione transferase FosA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5208
Polymers30,0562
Non-polymers4646
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-46 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.784, 67.208, 76.844
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

#1: Protein Glutathione transferase FosA / Fosfomycin resistance protein


Mass: 15027.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fosA, PA1129 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I4K6, glutathione transferase
#2: Chemical ChemComp-FCN / FOSFOMYCIN / 1,2-EPOXYPROPYLPHOSPHONIC ACID


Mass: 138.059 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O4P / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 85 mM K2HPO4 (pH 7.0), 41.5% pentaerythritol propoxylate 17/8 PO/OH (PEP629), 1mM MnCl2, 40 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5406 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.8→25.29 Å / Num. obs: 26765 / % possible obs: 99.27 % / Redundancy: 4.5 % / Biso Wilson estimate: 9.35 Å2 / Rpim(I) all: 0.0272 / Net I/σ(I): 21.5
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 1794 / Rpim(I) all: 0.08969

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→25.29 Å / SU ML: 0.145 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8099
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1938 1999 7.47 %
Rwork0.1664 24763 -
obs0.1685 26762 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 20 278 2422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552208
X-RAY DIFFRACTIONf_angle_d0.76222998
X-RAY DIFFRACTIONf_chiral_restr0.0506302
X-RAY DIFFRACTIONf_plane_restr0.0073394
X-RAY DIFFRACTIONf_dihedral_angle_d13.2919784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.19981340.1621660X-RAY DIFFRACTION94.17
1.85-1.890.22921370.16921697X-RAY DIFFRACTION96.83
1.89-1.950.22761400.16751739X-RAY DIFFRACTION99.58
1.95-2.010.19421410.15971747X-RAY DIFFRACTION99.47
2.01-2.090.19331430.1651754X-RAY DIFFRACTION100
2.09-2.170.19531420.1721765X-RAY DIFFRACTION100
2.17-2.270.19081420.16481770X-RAY DIFFRACTION99.84
2.27-2.390.19061420.16471753X-RAY DIFFRACTION100
2.39-2.540.1971430.17511768X-RAY DIFFRACTION100
2.54-2.730.20431440.19171791X-RAY DIFFRACTION100
2.73-3.010.21871450.18991779X-RAY DIFFRACTION100
3.01-3.440.18751450.17631797X-RAY DIFFRACTION100
3.44-4.330.17061470.14471832X-RAY DIFFRACTION100
4.33-25.290.17541540.14921911X-RAY DIFFRACTION99.81

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