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- PDB-1hgx: HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE (HGXPRTASE) -

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Basic information

Entry
Database: PDB / ID: 1hgx
TitleHYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE (HGXPRTASE)
ComponentsHYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE (GLYCOSYLTRANSFERASE) / TRANSFERASE / GLYCOSYLTRANSFERASE / PURINE SALVAGE
Function / homology
Function and homology information


xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Hypoxanthine-guanine-xanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesTritrichomonas foetus (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSomoza, J.R. / Wang, C.C. / Fletterick, R.J.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structure of the hypoxanthine-guanine-xanthine phosphoribosyltransferase from the protozoan parasite Tritrichomonas foetus.
Authors: Somoza, J.R. / Chin, M.S. / Focia, P.J. / Wang, C.C. / Fletterick, R.J.
#1: Journal: Mol.Biochem.Parasitol. / Year: 1994
Title: Isolation, Sequencing and Expression of the Gene Encoding Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase of Tritrichomonas Foetus
Authors: Chin, M.S. / Wang, C.C.
History
DepositionMar 12, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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-XANTHINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6884
Polymers42,2292
Non-polymers4592
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-30 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.960, 74.920, 55.720
Angle α, β, γ (deg.)90.00, 110.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE / HGXPRTASE


Mass: 21114.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tritrichomonas foetus (eukaryote) / Strain: KV1 / Plasmid: PBACE / Production host: Escherichia coli (E. coli)
References: UniProt: P51900, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop / PH range low: 6.8 / PH range high: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 Mammonium salfate1reservoir
20.1 MBis-Tris1reservoir
328-32 %(w/v)PEG80001reservoir
410 mg/mlHGX-PRTase1drop
550 mMBis-Tris1drop
66 mM1dropMgCl2

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 16, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 27314 / % possible obs: 91.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.063
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 9999 Å / Num. measured all: 97259
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.96 Å / % possible obs: 55.6 % / Rmerge(I) obs: 0.38

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN HGPRTASE

Resolution: 1.9→6 Å / σ(F): -3
Details: THE TEMPERATURE FACTORS FOR THE FOLLOWING RESIDUES ARE HIGH, AND THE PLACEMENT OF THESE RESIDUES SHOULD BE VIEWED WITH SKEPTICISM: GLU A179 MET B 7 CYS B 71
RfactorNum. reflection% reflection
Rfree0.234 -10 %
Rwork0.175 --
obs0.175 26229 -
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2650 0 29 134 2813
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d1.42
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1GMP.PARAMGMP.TOP
X-RAY DIFFRACTION2SOLVENT.PARAMSOLVENT.TOP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.42
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.42

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