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- PDB-8fwy: Crystal structure of the Trypanosoma cruzi hypoxanthine-guanine-x... -

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Basic information

Entry
Database: PDB / ID: 8fwy
TitleCrystal structure of the Trypanosoma cruzi hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT), isoform D, bound to the dead-end complex xanthine and pyrophosphate
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / Hypoxanthine-guanine-xanthine phosphoribosyltransferase / HGXPRT
Function / homology
Function and homology information


guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / magnesium ion binding / membrane / cytosol
Similarity search - Function
: / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
Similarity search - Domain/homology
PHOSPHATE ION / XANTHINE / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsHughes, R. / Meneely, K.M. / Glockzin, K. / Tyler, P.C. / Lamb, A.L. / Meek, T.D. / Katzfuss, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127807 United States
CitationJournal: Biochemistry / Year: 2023
Title: Kinetic and Structural Characterization of Trypanosoma cruzi Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferases and Repurposing of Transition-State Analogue Inhibitors.
Authors: Glockzin, K. / Meneely, K.M. / Hughes, R. / Maatouk, S.W. / Pina, G.E. / Suthagar, K. / Clinch, K. / Buckler, J.N. / Lamb, A.L. / Tyler, P.C. / Meek, T.D. / Katzfuss, A.
History
DepositionJan 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 1.3Nov 22, 2023Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2606
Polymers51,7662
Non-polymers4944
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-21 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.229, 81.015, 90.685
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 Hypoxanthine-guanine phosphoribosyltransferase


Mass: 25882.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Gene: ECC02_007666 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A7J6XZA2, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M lithium sufate, 24% PEG3350, 0.1 M HEPES, pH 8.0

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97937 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.54→48.34 Å / Num. obs: 60863 / % possible obs: 91.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 21.8 Å2 / Rpim(I) all: 0.04 / Net I/σ(I): 10.7
Reflection shellResolution: 1.54→1.57 Å / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1536 / Rpim(I) all: 0.494

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TC2

1tc2


Resolution: 1.54→48.34 Å / SU ML: 0.1622 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9298
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1983 3117 5.13 %
Rwork0.1891 57648 -
obs0.1895 60765 91.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.59 Å2
Refinement stepCycle: LAST / Resolution: 1.54→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3407 0 32 255 3694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01733519
X-RAY DIFFRACTIONf_angle_d1.75534766
X-RAY DIFFRACTIONf_chiral_restr0.564534
X-RAY DIFFRACTIONf_plane_restr0.0069609
X-RAY DIFFRACTIONf_dihedral_angle_d22.59951304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.3428650.31121403X-RAY DIFFRACTION49.95
1.56-1.590.319990.29521691X-RAY DIFFRACTION59.91
1.59-1.620.2943970.27641916X-RAY DIFFRACTION67.62
1.62-1.650.24571030.27112087X-RAY DIFFRACTION73.61
1.65-1.680.29261270.25682251X-RAY DIFFRACTION80.09
1.68-1.710.25391530.24692532X-RAY DIFFRACTION89.98
1.71-1.750.25141410.2272737X-RAY DIFFRACTION97.53
1.75-1.790.27241470.21972798X-RAY DIFFRACTION98.53
1.79-1.840.23771640.20972835X-RAY DIFFRACTION99.97
1.84-1.890.22471420.20512833X-RAY DIFFRACTION99.93
1.89-1.940.20061530.20292861X-RAY DIFFRACTION99.97
1.94-20.20031470.19852803X-RAY DIFFRACTION100
2-2.080.20071630.19772842X-RAY DIFFRACTION99.97
2.08-2.160.19771680.1842824X-RAY DIFFRACTION99.93
2.16-2.260.19241620.17312846X-RAY DIFFRACTION100
2.26-2.380.17721510.18232852X-RAY DIFFRACTION99.93
2.38-2.520.20031540.18032868X-RAY DIFFRACTION100
2.52-2.720.191510.19732877X-RAY DIFFRACTION100
2.72-2.990.20841420.18512888X-RAY DIFFRACTION99.93
2.99-3.430.20441570.18252901X-RAY DIFFRACTION100
3.43-4.320.16041610.16052948X-RAY DIFFRACTION99.94
4.32-48.340.19011700.18633055X-RAY DIFFRACTION99.85

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