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- PDB-1qk3: TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qk3 | ||||||
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Title | TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE GMP COMPLEX | ||||||
![]() | HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE | ||||||
![]() | TRANSFERASE / GLYCOSYLTRANSFERASE / PURINE SALVAGE | ||||||
Function / homology | ![]() xanthine phosphoribosyltransferase / xanthine phosphoribosyltransferase activity / XMP salvage / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage ...xanthine phosphoribosyltransferase / xanthine phosphoribosyltransferase activity / XMP salvage / 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. / Borhani, D.W. | ||||||
![]() | ![]() 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. / Borhani, D.W. #1: ![]() Title: Crystal Structure of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two Mg2+ Ions Bound: Insights Into the Catalytic Mechanism Authors: Heroux, A. / White, E.L. / Ross, L.J. / Davis, R.L. / Borhani, D.W. #2: Journal: Gene / Year: 1994 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 | ![]() | 206.8 KB | Display | ![]() |
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PDB format | ![]() | 164.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 43.9 KB | Display | |
Data in CIF | ![]() | 62.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qk4C ![]() 1hmpS S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE BIOMOLECULE CONSISTS OF A HOMO- TETRAMERIC COMPLEXOF BIOPOLYMERS |
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Components
#1: Protein | Mass: 26705.502 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q26997, hypoxanthine phosphoribosyltransferase #2: Chemical | ChemComp-5GP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 5 Details: 15% PEG 8000, 100 MM KPO4 (PH 5-6), 0.25% BETA-OCTYLGLUCOPYRANOSIDE, 1 MM GMP, 277 K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6 / PH range high: 5 | ||||||||||||||||||||||||||||||
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: ADSC CCD / Detector: CCD / Date: Jun 15, 1996 / Details: RH MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→12.5 Å / Num. obs: 108535 / % possible obs: 96.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.053 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.459 / % possible all: 85.3 |
Reflection | *PLUS Num. measured all: 302104 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS % possible obs: 85.3 % / Rmerge(I) obs: 0.459 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HMP, SUBUNIT A, WITHOUT LOOPS, WATERS, OR GMP Resolution: 1.65→12.5 Å / SU B: 1.27012 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11491 / ESU R Free: 0.10941 Details: THE STRUCTURE WAS FIRST REFINED USING X-XPLOR. REFMAC AND ARP WERE USED TO FINISH THE REFINEMENT, USING THE X-PLOR-CALCULATED BULK SOLVENT CORRECTION.
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Displacement parameters | Biso mean: 22.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→12.5 Å
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Refine LS restraints |
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