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- PDB-7san: Crystal structure of human hypoxanthine guanine phosphoribzosyltr... -

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Basic information

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


adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase ...adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / IMP metabolic process / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / grooming behavior / IMP salvage / Purine salvage / striatum development / AMP salvage / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / Azathioprine ADME / purine ribonucleoside salvage / dendrite morphogenesis / dopamine metabolic process / central nervous system neuron development / response to amphetamine / locomotory behavior / T cell mediated cytotoxicity / protein homotetramerization / nucleotide binding / magnesium ion binding / extracellular exosome / identical protein 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58155523622 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 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3138
Polymers97,5404
Non-polymers1,7734
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, MALS AND OTHER CRYSTAL STRUCTURES
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-34 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.818, 93.743, 130.46
Angle α, β, γ (deg.)90.0, 90.0, 90.0
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 / / HGPRT / HGPRTase


Mass: 24385.021 Da / Num. of mol.: 4 / Mutation: C22A, C105A, C205A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPRT1, HPRT / Production host: Escherichia coli (E. coli)
References: UniProt: P00492, 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.: 4 / Source method: obtained synthetically / Formula: C11H19N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Bis-tris propane, pH 7.4, 0.1 M sodium citrate, 17.5% PEG 3350
Temp details: INCUBATOR

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.58→49.17 Å / Num. obs: 29515 / % possible obs: 99.6 % / Redundancy: 11.2 % / Biso Wilson estimate: 50.4065251836 Å2 / CC1/2: 0.97 / Net I/σ(I): 12.66
Reflection shellResolution: 2.58→2.67 Å / Redundancy: 7.5 % / Num. unique obs: 2806 / CC1/2: 0.9 / % possible all: 96.19

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
BLU-MAXdata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GEP

3gep


Resolution: 2.58155523622→49.1672764131 Å / SU ML: 0.337542685968 / Cross valid method: FREE R-VALUE / σ(F): 1.34356605534 / Phase error: 29.7639423357
RfactorNum. reflection% reflection
Rfree0.257283736354 1994 6.7903967308 %
Rwork0.203344261289 27371 -
obs0.206998652186 29365 99.4378788392 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.9478388429 Å2
Refinement stepCycle: LAST / Resolution: 2.58155523622→49.1672764131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 112 60 6454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002666393837066567
X-RAY DIFFRACTIONf_angle_d0.6822950759728900
X-RAY DIFFRACTIONf_chiral_restr0.0252463322234993
X-RAY DIFFRACTIONf_plane_restr0.003835134316681119
X-RAY DIFFRACTIONf_dihedral_angle_d13.6613343072525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5816-2.64610.3365026346641340.2712446297441841X-RAY DIFFRACTION94.6788111218
2.6461-2.71760.3475118045691410.2513223766621930X-RAY DIFFRACTION100
2.7176-2.79760.3129541977291400.2503402704581928X-RAY DIFFRACTION99.8551424433
2.7976-2.88790.3340080724571410.2429766965841933X-RAY DIFFRACTION100
2.8879-2.99110.3403934322671410.2332285534321944X-RAY DIFFRACTION99.9520613615
2.9911-3.11080.2819626084721420.2306512835621943X-RAY DIFFRACTION99.9520613615
3.1108-3.25240.3059986799741420.2283667440751951X-RAY DIFFRACTION100
3.2524-3.42380.2782127958451420.2269450024671956X-RAY DIFFRACTION99.857210852
3.4238-3.63830.2761924784521430.2196132065771940X-RAY DIFFRACTION99.9520153551
3.6383-3.91910.2616304961221430.1954250450371964X-RAY DIFFRACTION99.8578199052
3.9191-4.31330.2373392934421430.179122327011969X-RAY DIFFRACTION99.9053926206
4.3133-4.93690.1843403269881440.1571608958641981X-RAY DIFFRACTION99.9529633114
4.9369-6.2180.2433791219571470.1947111156342012X-RAY DIFFRACTION99.9074502545
6.218-49.16720.2157699736341510.1886575495072079X-RAY DIFFRACTION98.3245149912

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