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Open data
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Basic information
Entry | Database: PDB / ID: 1lhr | ||||||
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Title | Crystal Structure of Pyridoxal Kinase complexed with ATP | ||||||
![]() | Pyridoxal kinase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 131.9 KB | Display | ![]() |
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PDB format | ![]() | 103.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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: Chemical | #3: Chemical | #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.86 % | ||||||||||||||||||||||||
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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: SEALED TUBE / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 21, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.6→20 Å / Num. all: 22694 / Num. obs: 22694 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.124 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.6→2.66 Å / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1491 / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 102919 |
Reflection shell | *PLUS % possible obs: 99.7 % |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree![]() ![]() | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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