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

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Basic information

Entry
Database: PDB / ID: 8fwz
TitleCrystal structure of the Trypanosoma cruzi hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT), isoform D, bound to Hydroxypropyl-Lin-ImmH Phosphonate
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE/INHIBITOR / Hypoxanthine-guanine-xanthine phosphoribosyltransferase / inhibitor / HGXPRT / TRANSFERASE-INHIBITOR complex
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 / Chem-YCE / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHughes, R. / Meneely, K.M. / Glockzin, K. / Clinch, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,4655
Polymers51,7662
Non-polymers6993
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-17 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.881, 80.066, 89.710
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-YCE / [(2R)-2-hydroxy-3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}propyl]phosphonic acid


Mass: 302.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N4O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M lithium sulfate, 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: 1.0332 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.65→49.8 Å / Num. obs: 52539 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 26.41 Å2 / Rpim(I) all: 0.055 / Net I/σ(I): 13.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2598 / Rpim(I) all: 0.414 / % possible all: 100

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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: 1.65→49.8 Å / SU ML: 0.1759 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8364
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2088 2646 5.05 %
Rwork0.1985 49792 -
obs0.199 52438 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.27 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 45 178 3602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01613505
X-RAY DIFFRACTIONf_angle_d1.80374750
X-RAY DIFFRACTIONf_chiral_restr0.5154532
X-RAY DIFFRACTIONf_plane_restr0.0067605
X-RAY DIFFRACTIONf_dihedral_angle_d22.69371302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.27431220.26642574X-RAY DIFFRACTION98.14
1.68-1.710.27721650.25522569X-RAY DIFFRACTION99.93
1.71-1.750.23111200.24672595X-RAY DIFFRACTION99.93
1.75-1.790.27371410.24642604X-RAY DIFFRACTION99.85
1.79-1.830.27641430.2262591X-RAY DIFFRACTION99.93
1.83-1.870.24321580.21472574X-RAY DIFFRACTION99.74
1.87-1.920.23191330.20832594X-RAY DIFFRACTION99.93
1.92-1.980.21221350.20332586X-RAY DIFFRACTION99.93
1.98-2.040.21981380.20482632X-RAY DIFFRACTION100
2.04-2.120.21821400.20012592X-RAY DIFFRACTION100
2.12-2.20.20921170.19872629X-RAY DIFFRACTION99.78
2.2-2.30.21771510.1982614X-RAY DIFFRACTION99.89
2.3-2.420.21751410.19492619X-RAY DIFFRACTION100
2.42-2.570.24071460.20222629X-RAY DIFFRACTION99.82
2.57-2.770.20291280.20452643X-RAY DIFFRACTION99.78
2.77-3.050.22141540.20732613X-RAY DIFFRACTION99.43
3.05-3.490.20891420.19582636X-RAY DIFFRACTION99.11
3.49-4.40.19141370.17282664X-RAY DIFFRACTION98.66
4.4-49.80.17721350.19642834X-RAY DIFFRACTION99.43

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