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- PDB-9e47: Crystal Structure of FosA from Pseudomonas aeruginosa with Mangan... -

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Basic information

Entry
Database: PDB / ID: 9.0E+47
TitleCrystal Structure of FosA from Pseudomonas aeruginosa with Manganese and (1-Hydroxypropan-2-yl)phosphonic acid
ComponentsGlutathione transferase FosA
KeywordsTRANSFERASE / glutathione transfersase / homodimer / inhibitor
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
: / : / [(2S)-1-hydroxypropan-2-yl]phosphonic acid / Glutathione transferase FosA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsWiltsie, V. / Thompson, M.K. / Gilbert, N.C. / Garneau-Tsodikova, S. / Thamban Chandrika, N.
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 (1-Hydroxypropan-2-yl)phosphonic acid
Authors: Wiltsie, V. / Thompson, M.K. / Gilbert, N.C. / Garneau-Tsodikova, S. / Thamban Chandrika, N.
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)30,5248
Polymers30,0562
Non-polymers4686
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-47 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.417, 64.907, 74.356
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-YRQ / [(2S)-1-hydroxypropan-2-yl]phosphonic acid


Mass: 140.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O4P / 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.: 119 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 85 mM K2HPO4 (pH 7.0), 40.5% PEP629, 1 mM MnCl2, and 40 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.59→37.18 Å / Num. obs: 84580 / % possible obs: 97.17 % / Redundancy: 5.9 % / Biso Wilson estimate: 20.01 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.36
Reflection shellResolution: 1.59→1.63 Å / Num. unique obs: 837 / Rrim(I) all: 7.847

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→37.18 Å / SU ML: 0.1526 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2178
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2112 2000 5.6 %
Rwork0.1878 33711 -
obs0.1891 35711 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.31 Å2
Refinement stepCycle: LAST / Resolution: 1.59→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 20 119 2263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542209
X-RAY DIFFRACTIONf_angle_d0.78362996
X-RAY DIFFRACTIONf_chiral_restr0.0522300
X-RAY DIFFRACTIONf_plane_restr0.0071395
X-RAY DIFFRACTIONf_dihedral_angle_d13.6568780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.3041150.26391938X-RAY DIFFRACTION79.33
1.63-1.670.22171250.22222113X-RAY DIFFRACTION86.78
1.67-1.720.25641390.20872322X-RAY DIFFRACTION95.46
1.72-1.780.2411440.19752440X-RAY DIFFRACTION99.88
1.78-1.840.20161450.19772452X-RAY DIFFRACTION99.96
1.84-1.920.22021460.19852455X-RAY DIFFRACTION99.96
1.92-20.21991450.18392439X-RAY DIFFRACTION100
2-2.110.20641450.19472463X-RAY DIFFRACTION99.66
2.11-2.240.2351460.18762453X-RAY DIFFRACTION99.24
2.24-2.410.24791480.19582488X-RAY DIFFRACTION99.96
2.41-2.660.2251470.21032478X-RAY DIFFRACTION100
2.66-3.040.21641480.21152483X-RAY DIFFRACTION99.92
3.04-3.830.19341500.1782530X-RAY DIFFRACTION99.81
3.83-37.180.18261570.15952657X-RAY DIFFRACTION99.89

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