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Yorodumi- PDB-1qk5: TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qk5 | ||||||
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Title | TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH XMP, PYROPHOSPHATE AND TWO MG2+ IONS | ||||||
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: 1.6 Å | ||||||
Authors | Heroux, A. / White, E.L. / Ross, L.J. / Davis, R.L. / Borhani, D.W. | ||||||
Citation | 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. #1: 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. #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 | 1qk5.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qk5.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/1qk5 ftp://data.pdbj.org/pub/pdb/validation_reports/qk/1qk5 | HTTPS FTP |
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-Related structure data
Related structure data | 1qk3S S: Starting model for refinement |
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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: (Code: given Matrix: (-0.951065, 0.000778, -0.308991), Vector: Details | THE BIOMOLECULE CONSISTS OF A HOMO- TETRAMERIC COMPLEXOF BIOPOLYMERSSUBUNITS C AND D OF THE HGPRT HOMOTETRAMER ARE GENERATEDBY ROTATION OF SUBUNITS A AND B ABOUT THECRYSTALLOGRAPHIC 2- FOLD AXIS PARALLEL TO B. | |
-Components
#1: Protein | Mass: 26661.492 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: RH / Plasmid: PETC1-D150A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q26997, hypoxanthine phosphoribosyltransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / #5: 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: 2.09 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 8.5 Details: 30% PEG 4000, 100 MM TRIS.CL (PH 8.5), 200 MM LI2SO4, 0.25 % BETA-OCTYLGLUCOPYRANOSIDE. THE CRYSTAL WAS GROWN IN THE PRESENCE OF 1 MM XANTHINE, 1 MM PRPP AND 10 MM MGCL2 AT 277 K. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions 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: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: PRINCETON SCIENTIFIC INSTRUMENTS 2K CCD / Detector: CCD / Date: Feb 15, 1998 / Details: PT-COATED MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→13 Å / Num. obs: 58200 / % possible obs: 98 % / Redundancy: 4.2 % / Biso Wilson estimate: 24.14 Å2 / Rsym value: 0.076 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.373 / % possible all: 93.9 |
Reflection | *PLUS Num. measured all: 245248 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 93.9 % / Rmerge(I) obs: 0.373 |
-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: 1.6→13 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11647 / ESU R Free: 0.11121 Details: NO RESTRAINTS WERE IMPOSED ON THE ATOMS OF THE PYROPHOSPHATE GROUPS OR MAGNESIUM CATIONS.
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Displacement parameters | Biso mean: 25.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→13 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.234 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |