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- PDB-1gc5: CRYSTAL STRUCTURE OF A NOVEL ADP-DEPENDENT GLUCOKINASE FROM THERM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gc5 | ||||||
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Title | CRYSTAL STRUCTURE OF A NOVEL ADP-DEPENDENT GLUCOKINASE FROM THERMOCOCCUS LITORALIS | ||||||
![]() | ADP-DEPENDENT GLUCOKINASE | ||||||
![]() | TRANSFERASE / ALFA/BETA SANDWICHS / INDUCED-FITTING | ||||||
Function / homology | ![]() ADP-specific glucose/glucosamine kinase / ADP-specific glucokinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / glucokinase activity / glycolytic process / glucose metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ito, S. / Fushinobu, S. / Yoshioka, I. / Koga, S. / Matsuzawa, H. / Wakagi, T. | ||||||
![]() | ![]() Title: Structural Basis for the ADP-Specificity of a Novel Glucokinase from a Hyperthermophilic Archaeon Authors: Ito, S. / Fushinobu, S. / Yoshioka, I. / Koga, S. / Matsuzawa, H. / Wakagi, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.2 KB | Display | ![]() |
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PDB format | ![]() | 82 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 771.2 KB | Display | ![]() |
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Full document | ![]() | 791.4 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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 monomer. |
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Components
#1: Protein | Mass: 53618.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q7M537, ADP-specific glucose/glucosamine kinase |
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#2: Chemical | ChemComp-ADP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.79 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: potassium chloride, citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 286 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 167633 / Num. obs: 46477 / % possible obs: 77 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.177 / % possible all: 45.8 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 77 % / Num. measured all: 167633 |
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Processing
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Refinement | Resolution: 2.3→6 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor obs: 0.204 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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