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- PDB-9e43: Crystal Structure of FosA from Pseudomonas aeruginosa with Mangan... -

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Basic information

Entry
Database: PDB / ID: 9.0E+43
TitleCrystal Structure of FosA from Pseudomonas aeruginosa with Manganese and Phosphonoacetate
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
: / : / PHOSPHONOACETIC ACID / Glutathione transferase FosA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsWiltsie, V. / Thompson, M.K. / Gilbert, N.C.
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 Phosphonoacetate
Authors: Wiltsie, V. / Thompson, M.K. / Gilbert, N.C.
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
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-54 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.293, 65.065, 74.164
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-PAE / PHOSPHONOACETIC ACID


Mass: 140.032 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5O5P / 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.: 186 / 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: 44.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 76 mM K2HPO4 (pH 7.0), 40% PEP629, 1mM 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: 1.41→37.08 Å / Num. obs: 135042 / % possible obs: 99.68 % / Redundancy: 5.7 % / Biso Wilson estimate: 15.44 Å2 / Rmerge(I) obs: 0.07891 / Net I/σ(I): 9.53
Reflection shellResolution: 1.41→1.45 Å / Rmerge(I) obs: 6.316 / Num. unique obs: 1417

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→37.08 Å / SU ML: 0.1333 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8403
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1944 2000 3.84 %
Rwork0.1765 50103 -
obs0.1772 52103 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.97 Å2
Refinement stepCycle: LAST / Resolution: 1.41→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 20 186 2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482198
X-RAY DIFFRACTIONf_angle_d0.77892978
X-RAY DIFFRACTIONf_chiral_restr0.0828296
X-RAY DIFFRACTIONf_plane_restr0.0073394
X-RAY DIFFRACTIONf_dihedral_angle_d15.1602774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.450.30571360.24573398X-RAY DIFFRACTION96.43
1.45-1.480.25151410.22663536X-RAY DIFFRACTION99.84
1.48-1.530.22621420.19613564X-RAY DIFFRACTION100
1.53-1.580.19661410.18163531X-RAY DIFFRACTION100
1.58-1.630.16341420.16763558X-RAY DIFFRACTION99.97
1.63-1.70.17911410.1723537X-RAY DIFFRACTION100
1.7-1.780.20731430.17613575X-RAY DIFFRACTION99.97
1.78-1.870.18411410.17823544X-RAY DIFFRACTION99.97
1.87-1.990.18781440.16793600X-RAY DIFFRACTION100
1.99-2.140.18521430.17533594X-RAY DIFFRACTION99.89
2.14-2.360.19781430.17533586X-RAY DIFFRACTION99.92
2.36-2.70.2091450.19253603X-RAY DIFFRACTION99.68
2.7-3.40.18411460.18363662X-RAY DIFFRACTION99.97
3.4-37.080.1881520.15783815X-RAY DIFFRACTION99.87

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