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- PDB-1qk4: TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qk4 | ||||||
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Title | TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE IMP 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 | ![]() | 198.8 KB | Display | ![]() |
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PDB format | ![]() | 156.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 41.9 KB | Display | |
Data in CIF | ![]() | 58 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qk3SC 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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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-IMP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 8.5 Details: 30% PEG 4000, 100 MM TRIS (PH 8.5), 200 MM LI2SO4, 0.25 % BETA-OCTYLGLUCOPYRANOSIDE 1 MM IMP, 277 K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
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: Jun 15, 1997 / Details: PT-COATED MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→12.5 Å / Num. obs: 74791 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 19.863 Å2 / Rsym value: 0.076 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.383 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 305699 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.383 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QK3, SUBUNIT A, WITHOUT LOOPS, WATERS, OR GMP Resolution: 1.9→12.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16026 / ESU R Free: 0.15181 Details: X-PLOR WAS USED IN THE EARLY STAGES OF REFINEMENT. 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: 22.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→12.5 Å
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Refine LS restraints |
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