+Open data
-Basic information
Entry | Database: PDB / ID: 1lhr | ||||||
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Title | Crystal Structure of Pyridoxal Kinase complexed with ATP | ||||||
Components | Pyridoxal kinase | ||||||
Keywords | TRANSFERASE / ALPHA-BETA structure / complexed with ATP | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.6 Å | ||||||
Authors | Liang, D.C. / Jiang, T. / Li, M.H. | ||||||
Citation | 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. / Jiang, T. / Liang, D.C. #1: 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 | 1lhr.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lhr.ent.gz | 103.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lhr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lhr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1lhr_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1lhr_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 1lhr_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/1lhr ftp://data.pdbj.org/pub/pdb/validation_reports/lh/1lhr | HTTPS FTP |
-Related 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 formed by the two peptide chains in the asymmetric unit. |
-Components
#1: Protein | Mass: 34860.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Tissue: brain / References: UniProt: P82197, pyridoxal kinase #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.55 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: 1.5418 Å / Relative weight: 1 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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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: 0.225 / Rfactor Rwork: 0.196 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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