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Yorodumi- PDB-1rft: Crystal structure of pyridoxal kinase complexed with AMP-PCP and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rft | ||||||
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Title | Crystal structure of pyridoxal kinase complexed with AMP-PCP and pyridoxamine | ||||||
Components | Pyridoxal kinase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / phosphorylation / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Liang, D.-C. / Jiang, T. / Li, M.-H. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2004 Title: Conformational changes in the reaction of pyridoxal kinase Authors: Li, M.-H. / Kwok, F. / Chang, W.-R. / Liu, S.-Q. / Lo, S.C.L. / Zhang, J.-P. / Jiang, T. / Liang, D.-C. #1: Journal: J.Biol.Chem. / Year: 2002 Title: Crystal Structure of Brain Pyridoxal Kinase, a Novel Member of the Ribokinase Superfamily Authors: Li, M.-H. / Kwok, F. / Chang, W.-R. / Lau, C.-K. / Zhang, J.-P. / Lo, S.C.L. / Jiang, T. / Liang, D.-C. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Crystallization and preliminary crystallographic studies of pyridoxal kinase from sheep brain Authors: Li, M.-H. / Kwok, F. / An, X.-M. / Chang, W.-R. / Lau, C.-K. / Zhang, J.-P. / Liu, S.-Q. / Leung, Y.-C. / Jiang, T. / Liang, D.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rft.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rft.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 1rft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/1rft ftp://data.pdbj.org/pub/pdb/validation_reports/rf/1rft | HTTPS FTP |
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-Related structure data
Related structure data | 1rfuC 1rfvC 1lhpS 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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Details | The biological assembly is a dimer, and the two monomers that form the dimer are related by a crystallographic 2-fold axis |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34860.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: P82197, pyridoxal kinase |
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-Non-polymers , 5 types, 130 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-ACP / |
#5: Chemical | ChemComp-PXM / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.09 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: ammonium sulphate, potassium phosphate, pyridoxamine, AMP-PCP, zinc acetate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: SEALED TUBE / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 2002 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 9170 / Num. obs: 9133 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.8→2.86 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 3.4 / Num. unique all: 591 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LHP Resolution: 2.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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