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- PDB-8fx2: Crystal structure of the Trypanosoma cruzi hypoxanthine-guanine-x... -

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Basic information

Entry
Database: PDB / ID: 8fx2
TitleCrystal structure of the Trypanosoma cruzi hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT), isoform D, bound to Immucillin-HP
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / Hypoxanthine-guanine-xanthine phosphoribosyltransferase / inhibitor / HGXPRT
Function / homology
Function and homology information


guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / nucleotide binding / magnesium ion binding / membrane / cytosol
Similarity search - Function
: / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
Similarity search - Domain/homology
Chem-IRP / 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. / Suthagar, 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)52,4584
Polymers51,7662
Non-polymers6922
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-14 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.083, 80.478, 89.877
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-IRP / (1S)-1(9-DEAZAHYPOXANTHIN-9YL)1,4-DIDEOXY-1,4-IMINO-D-RIBITOL-5-PHOSPHATE


Mass: 346.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N4O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
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: 1.54→49.95 Å / Num. obs: 56370 / % possible obs: 86.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 21.59 Å2 / Rpim(I) all: 0.052 / Net I/σ(I): 11.4
Reflection shellResolution: 1.54→1.57 Å / Num. unique obs: 1254 / Rpim(I) all: 0.475

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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→49.95 Å / SU ML: 0.1627 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3068
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1977 2890 5.14 %
Rwork0.1833 53386 -
obs0.1841 56276 86.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.71 Å2
Refinement stepCycle: LAST / Resolution: 1.54→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 46 317 3754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01643512
X-RAY DIFFRACTIONf_angle_d1.75044761
X-RAY DIFFRACTIONf_chiral_restr0.0933539
X-RAY DIFFRACTIONf_plane_restr0.0068604
X-RAY DIFFRACTIONf_dihedral_angle_d23.01851295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.570.3698600.31741114X-RAY DIFFRACTION38.39
1.57-1.590.3782700.29571299X-RAY DIFFRACTION44.67
1.59-1.620.3077810.27041495X-RAY DIFFRACTION51.27
1.62-1.650.2862910.26631673X-RAY DIFFRACTION58.03
1.65-1.690.28311060.24731944X-RAY DIFFRACTION66.45
1.69-1.720.24951130.23292185X-RAY DIFFRACTION74.73
1.72-1.760.26781480.21252614X-RAY DIFFRACTION89.85
1.76-1.810.23521550.21132808X-RAY DIFFRACTION96.55
1.81-1.860.22511470.20012866X-RAY DIFFRACTION98.72
1.86-1.910.2071600.18922868X-RAY DIFFRACTION98.5
1.91-1.970.19211600.18752886X-RAY DIFFRACTION98.58
1.97-2.040.20741510.18192919X-RAY DIFFRACTION98.81
2.04-2.120.19731650.18062882X-RAY DIFFRACTION99.03
2.12-2.220.17891770.17092884X-RAY DIFFRACTION98.93
2.22-2.340.17641480.17232931X-RAY DIFFRACTION99.23
2.34-2.480.21381570.17482930X-RAY DIFFRACTION99.55
2.48-2.680.21321700.18282939X-RAY DIFFRACTION99.39
2.68-2.950.19061660.18152947X-RAY DIFFRACTION99.55
2.95-3.370.21241450.17873014X-RAY DIFFRACTION99.68
3.37-4.250.1821540.16113025X-RAY DIFFRACTION99.84
4.25-49.950.16761660.18643163X-RAY DIFFRACTION99.91

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