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- PDB-7sb7: Crystal structure of T. brucei hypoxanthine guanine phosphoribosy... -

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Basic information

Entry
Database: PDB / ID: 7sb7
TitleCrystal structure of T. brucei hypoxanthine guanine phosphoribosyltransferase in complex with (4S,7S)-7-hydroxy-4-((guanin-9-yl)methyl)-2,5-dioxaheptan-1,7-diphosphonate
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / inhibitor / complex / phosphonate / purine
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / nuclear lumen / glycosome / ciliary plasm / purine ribonucleoside salvage / nucleotide binding / metal ion binding ...hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / nuclear lumen / glycosome / ciliary plasm / purine ribonucleoside salvage / nucleotide binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Purine/pyrimidine phosphoribosyl transferases signature. / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
Similarity search - Domain/homology
Chem-8QI / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64716619036 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 24, 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
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3304
Polymers48,4442
Non-polymers8862
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-7 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.908, 93.983, 44.274
Angle α, β, γ (deg.)90.0, 109.125, 90.0
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Hypoxanthine-guanine phosphoribosyltransferase / HGPRT / HGPRTase


Mass: 24221.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HGPRT / Production host: Escherichia coli (E. coli)
References: UniProt: Q07010, 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.: 2 / Source method: obtained synthetically / Formula: C11H19N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M zinc acetate, 0.1 M sodium cadodylate, pH 6.5,10% 2-propanol. INDEX screen

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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: 2.647→46.9915 Å / Num. obs: 13024 / % possible obs: 98.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 37.170570164 Å2 / CC1/2: 0.98 / Net I/σ(I): 11.42
Reflection shellResolution: 2.647→2.742 Å / Num. unique obs: 1255 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5JV5

5jv5


Resolution: 2.64716619036→46.9915 Å / SU ML: 0.361731426277 / Cross valid method: FREE R-VALUE / σ(F): 1.37478520786 / Phase error: 29.1499503039
RfactorNum. reflection% reflection
Rfree0.253301141643 1295 9.94318181818 %
Rwork0.196150314606 11729 -
obs0.201972691184 13024 99.1398340565 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.2758084259 Å2
Refinement stepCycle: LAST / Resolution: 2.64716619036→46.9915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 56 70 2923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001915972783282947
X-RAY DIFFRACTIONf_angle_d0.5593358453314015
X-RAY DIFFRACTIONf_chiral_restr0.0209283148489465
X-RAY DIFFRACTIONf_plane_restr0.00258733260502501
X-RAY DIFFRACTIONf_dihedral_angle_d13.36255610751126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6472-2.75310.3340694089371410.2728071584351259X-RAY DIFFRACTION95.6937799043
2.7531-2.87840.3098323335561420.2309718852971295X-RAY DIFFRACTION99.7224149896
2.8784-3.03020.297438837531470.233664833811284X-RAY DIFFRACTION99.5824634656
3.0302-3.220.3222717054891490.2347113604051313X-RAY DIFFRACTION99.6591683708
3.22-3.46850.3045910307261390.2130724168641298X-RAY DIFFRACTION99.1718426501
3.4685-3.81740.2863825724381360.2017923237991311X-RAY DIFFRACTION99.4501718213
3.8174-4.36950.2070845765781510.1619958416941316X-RAY DIFFRACTION100
4.3695-5.50370.2122688678371460.1586114972291320X-RAY DIFFRACTION99.863760218
5.5037-46.90.1945946382871440.1825401734831333X-RAY DIFFRACTION99.1275167785

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