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Yorodumi- PDB-1pie: Crystal Structure of Lactococcus lactis Galactokinase Complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pie | ||||||
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Title | Crystal Structure of Lactococcus lactis Galactokinase Complexed with Galactose | ||||||
Components | Galactokinase | ||||||
Keywords | TRANSFERASE / galactose / galactosemia / kinase | ||||||
Function / homology | Function and homology information galactokinase / galactokinase activity / galactose metabolic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Thoden, J.B. / Holden, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Molecular Structure of Galactokinase Authors: Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pie.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pie.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pie_validation.pdf.gz | 463 KB | Display | wwPDB validaton report |
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Full document | 1pie_full_validation.pdf.gz | 489.1 KB | Display | |
Data in XML | 1pie_validation.xml.gz | 21 KB | Display | |
Data in CIF | 1pie_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/1pie ftp://data.pdbj.org/pub/pdb/validation_reports/pi/1pie | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46084.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Gene: GALK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9R7D7, galactokinase |
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#2: Sugar | ChemComp-GLA / |
#3: Chemical | ChemComp-PO4 / |
#4: 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: 2.67 Å3/Da / Density % sol: 53.86 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: batch / pH: 9 Details: sodium phosphate, potassium phosphate, CHES, galactose, pH 9, batch, temperature 277K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: microdialysis | ||||||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 0.97932, 0.97951, 0.96411, 0.65255 | |||||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Apr 4, 2003 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→20 Å / Num. all: 28616 / Num. obs: 28616 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rsym value: 0.067 / Net I/σ(I): 75.4 | |||||||||||||||
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 9.3 / Num. unique all: 2804 / Rsym value: 0.214 / % possible all: 99.5 | |||||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.067 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 99.5 % / Num. unique obs: 2804 / Rmerge(I) obs: 0.214 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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