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Yorodumi- PDB-1qk4: TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qk4 | ||||||
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Title | TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE IMP COMPLEX | ||||||
Components | HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / PURINE SALVAGE | ||||||
Function / homology | Function and homology information 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 | TOXOPLASMA GONDII (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Heroux, A. / White, E.L. / Ross, L.J. / Borhani, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 1999 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: Journal: Biochemistry / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qk4.cif.gz | 198.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qk4.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/1qk4 ftp://data.pdbj.org/pub/pdb/validation_reports/qk/1qk4 | HTTPS FTP |
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-Related structure data
Related structure data | 1qk3SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 |
-Components
#1: Protein | Mass: 26705.502 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: RH / Plasmid: PETC1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q26997, hypoxanthine phosphoribosyltransferase #2: Chemical | ChemComp-IMP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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