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- PDB-7scr: Crystal structure of trypanosome brucei hypoxanthine-guanine-xant... -

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Basic information

Entry
Database: PDB / ID: 7scr
TitleCrystal structure of trypanosome brucei hypoxanthine-guanine-xanthine phosphoribzosyltransferase in complex with (4S,7S)-7-hydroxy-4-((guanin-9-yl)methyl)-2,5-dioxaheptan-1,7-diphosphonate
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE/INHIBITOR / purine salvage / inhibitor / phosphonate / drug lead / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


xanthine phosphoribosyltransferase activity / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / glycosome / nuclear lumen / phosphate ion binding ...xanthine phosphoribosyltransferase activity / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / glycosome / nuclear lumen / phosphate ion binding / magnesium ion binding / cytoplasm / cytosol
Similarity search - Function
: / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
Similarity search - Domain/homology
Chem-8QI / Hypoxanthine-guanine phosphoribosyltransferase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12068485322 Å
AuthorsGuddat, L.W. / Keough, D.T.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1147368 Australia
CitationJournal: J.Med.Chem. / Year: 2022
Title: Stereo-Defined Acyclic Nucleoside Phosphonates are Selective and Potent Inhibitors of Parasite 6-Oxopurine Phosphoribosyltransferases.
Authors: Klejch, T. / Keough, D.T. / King, G. / Dolezelova, E. / Cesnek, M. / Budesinsky, M. / Zikova, A. / Janeba, Z. / Guddat, L.W. / Hockova, D.
History
DepositionSep 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxanthine-guanine phosphoribosyltransferase
C: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
E: Hypoxanthine-guanine phosphoribosyltransferase
F: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,20512
Polymers183,5466
Non-polymers2,6596
Water13,295738
1
A: Hypoxanthine-guanine phosphoribosyltransferase
E: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0684
Polymers61,1822
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint1 kcal/mol
Surface area17810 Å2
MethodPISA
2
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0684
Polymers61,1822
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-1 kcal/mol
Surface area18050 Å2
MethodPISA
3
B: Hypoxanthine-guanine phosphoribosyltransferase
F: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0684
Polymers61,1822
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint1 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.253, 107.298, 117.165
Angle α, β, γ (deg.)90.0, 96.759, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Hypoxanthine-guanine phosphoribosyltransferase / HGXPRT


Mass: 30590.955 Da / Num. of mol.: 6 / Mutation: F49V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: Tb10.70.6660 / Production host: Escherichia coli (E. coli)
References: UniProt: Q38CA1, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-8QI / ({(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-[(2S)-2-hydroxy-2-phosphonoethoxy]propoxy}methyl)phosphonic acid


Mass: 443.244 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H19N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 40.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane, 0.2 M lithium sulfate, 17.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.11→46.41 Å / Num. obs: 83246 / % possible obs: 96.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 28.9731619465 Å2 / CC1/2: 0.97 / Net I/σ(I): 10.5
Reflection shellResolution: 2.12→2.23 Å / Redundancy: 6.5 % / Num. unique obs: 9413 / CC1/2: 0.75 / % possible all: 80.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MXC

6mxc


Resolution: 2.12068485322→46.4 Å / SU ML: 0.333984735807 / Cross valid method: FREE R-VALUE / σ(F): 1.33787516497 / Phase error: 32.691214675
RfactorNum. reflection% reflection
Rfree0.266728263951 1983 2.40369463502 %
Rwork0.221325707627 80515 -
obs0.222445612984 82498 96.8354578961 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.648747756 Å2
Refinement stepCycle: LAST / Resolution: 2.12068485322→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10153 0 140 738 11031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023786749425810744
X-RAY DIFFRACTIONf_angle_d0.62786481809314597
X-RAY DIFFRACTIONf_chiral_restr0.0237988920821625
X-RAY DIFFRACTIONf_plane_restr0.002270087458251826
X-RAY DIFFRACTIONf_dihedral_angle_d13.12647272864248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1207-2.17370.385080087445900.3238474215753557X-RAY DIFFRACTION60.2113257388
2.1737-2.23250.3568214865241430.3062611136335856X-RAY DIFFRACTION99.4034797017
2.2325-2.29820.3439070328531460.3111846759965911X-RAY DIFFRACTION99.5725793194
2.2982-2.37240.3586575926741450.3120023810585923X-RAY DIFFRACTION99.6551157826
2.3724-2.45710.3641243996141440.3037826337985867X-RAY DIFFRACTION99.322538004
2.4571-2.55550.3560407254661450.294702611015868X-RAY DIFFRACTION99.1916859122
2.5555-2.67180.3062126517541460.2844902302975888X-RAY DIFFRACTION99.390545215
2.6718-2.81270.3768721790221440.2828222170225904X-RAY DIFFRACTION99.7525977239
2.8127-2.98880.3312325869051450.2373764176625897X-RAY DIFFRACTION99.867768595
2.9888-3.21960.2604474324931470.2114264245265976X-RAY DIFFRACTION99.9673469388
3.2196-3.54350.2410900680111460.1865280779715919X-RAY DIFFRACTION99.7696989636
3.5435-4.05590.2010624525641470.1686085864575956X-RAY DIFFRACTION99.8690885289
4.0559-5.1090.2030798081811460.1549058088275970X-RAY DIFFRACTION99.9019928128
5.109-46.40.1997231912511490.189800263566023X-RAY DIFFRACTION99.6448175654

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