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Open data
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Basic information
Entry | Database: PDB / ID: 1lhp | ||||||
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Title | Crystal Structure of Pyridoxal Kinase from Sheep Brain | ||||||
![]() | Pyridoxal kinase | ||||||
![]() | TRANSFERASE / ALPHA-BETA STRUCTURE | ||||||
Function / homology | ![]() pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / phosphorylation / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liang, D.C. / Jiang, T. / Li, M.H. | ||||||
![]() | ![]() 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. / Jiang, T. / Liang, D.C. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.1 KB | Display | ![]() |
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PDB format | ![]() | 102.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.4 KB | Display | ![]() |
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Full document | ![]() | 433.5 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Details | The biological assembly is a dimer formed by the two peptide chains in the asymmetric unit. |
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Components
#1: Protein | Mass: 34860.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.58 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 19, 2000 |
Radiation | Monochromator: Silicon crystal(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 42820 / Num. obs: 42820 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2812 / % possible all: 98.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 182984 |
Reflection shell | *PLUS % possible obs: 98.7 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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