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- PDB-1fsg: TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fsg | ||||||
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Title | TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH 9-DEAZAGUANINE, ALPHA-D-5-PHOSPHORIBOSYL-1-PYROPHOSPHATE (PRPP) AND TWO MG2+ IONS | ||||||
![]() | HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE | ||||||
![]() | TRANSFERASE / GLYCOSYLTRANSFERASE / PURINE SALVAGE | ||||||
Function / homology | ![]() xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Heroux, A. / White, E.L. / Ross, L.J. / Kuzin, A.P. / Borhani, D.W. | ||||||
![]() | ![]() Title: Substrate deformation in a hypoxanthine-guanine phosphoribosyltransferase ternary complex: the structural basis for catalysis. Authors: Heroux, A. / White, E.L. / Ross, L.J. / Kuzin, A.P. / Borhani, D.W. #1: ![]() Title: Crystal Structures of the Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase-GMP and -IMP Complexes:Comparison of purine binding Interactions with the XMP Complex Authors: Heroux, A. / White, E.L. / Ross, L.J. / Davis, R.L. / Borhani, D.W. #2: ![]() Title: Crystal Structure of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with XMP, Pyrophosphate, and Two Mg(2+) Ions Bound:Insights into the Catalytic Mechanism Authors: Heroux, A. / White, E.L. / Ross, L.J. / Borhani, D.W. #3: ![]() Title: Isolation and Sequencing of a Cdna Encoding the Hypoxanthine-Guanine Phosphoribosyltransferase from Toxoplasma Gondii Authors: Vasanthakumar, G. / van Ginkel, S. / Parish, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.4 KB | Display | ![]() |
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PDB format | ![]() | 198.4 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26705.502 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q26997, hypoxanthine phosphoribosyltransferase #2: Chemical | ChemComp-MG / #3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: THE PROTEIN (20 mg ml-1) WAS MIXED WITH A SOLUTION CONSISTING OF 30% PEG 4000, 100 MM TRIS.HCL (PH 8.0), 200 MM LI2SO4, and 0.5 % BETA-OCTYLGLUCOPYRANOSIDE. THE CRYSTAL WAS GROWN IN THE ...Details: THE PROTEIN (20 mg ml-1) WAS MIXED WITH A SOLUTION CONSISTING OF 30% PEG 4000, 100 MM TRIS.HCL (PH 8.0), 200 MM LI2SO4, and 0.5 % BETA-OCTYLGLUCOPYRANOSIDE. THE CRYSTAL WAS GROWN IN THE PRESENCE OF 2 MM 9-DEAZAGUANINE, 2 MM PRPP AND 10 MM MGCL2 AT 277 K. THE CRYSTAL GREW IN 2 DAYS., VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃Details: drop was mixed with an equal volume of reservoir solution | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1999 / Details: RH-COATED MIRROR |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.783 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→35 Å / Num. all: 220504 / Num. obs: 220504 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 7.435 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.05→1.08 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.8 / Num. unique all: 16129 / Rsym value: 0.555 / % possible all: 99.7 |
Reflection | *PLUS Num. obs: 220433 / Num. measured all: 915734 |
Reflection shell | *PLUS % possible obs: 99.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: UNPUBLISHED T. GONDII HGPRT-GMP COMPLEX STRUCTURE. LOOPS, WATERS AND GMP WERE REMOVED FROM ALL SUBUNITS OF THE MOLECULAR REPLACEMENT MODEL. Resolution: 1.05→35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Refinement with X-PLOR, then REFMAC and ARP alternated with manual rebuilding in O to reduce the free-R to 20.2% (35-1.05A). The model contained at that point alternate conformations, a CIS- ...Details: Refinement with X-PLOR, then REFMAC and ARP alternated with manual rebuilding in O to reduce the free-R to 20.2% (35-1.05A). The model contained at that point alternate conformations, a CIS-peptide bond (Leu78-Lys79), and the active site ligands, all of which were placed in unambiguous electron density. Refinement continued with SHELX-97, with refinement of anisotropic temperature factors. Riding hydrogen atoms were added in the latter stages. NO RESTRAINTS WERE IMPOSED ON THE ATOMS OF 9-DEAZAGUANINE, PHOSPHORIBOSYLPYROPHOSPHATE, THE MAGNESIUM CATIONS AND THEIR SURROUNDING WATER MOLECULES IN THE LATTER STAGES OF THE REFINEMENT.
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Solvent computation | Solvent model: SHELX SWAT | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→35 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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