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- PDB-1ex6: CRYSTAL STRUCTURE OF UNLIGANDED FORM OF GUANYLATE KINASE FROM YEAST -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ex6 | ||||||
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Title | CRYSTAL STRUCTURE OF UNLIGANDED FORM OF GUANYLATE KINASE FROM YEAST | ||||||
![]() | GUANYLATE KINASE | ||||||
![]() | TRANSFERASE / GUANYLATE KINASE / SUBSTRATE-INDUCED FIT / DOMAIN MOVEMENT / ATP / GMP / SUBSTRATE SPECIFICITY | ||||||
Function / homology | ![]() Azathioprine ADME / GDP biosynthetic process / guanylate kinase / purine nucleotide metabolic process / Interconversion of nucleotide di- and triphosphates / guanylate kinase activity / phosphorylation / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Blaszczyk, J. / Ji, X. | ||||||
![]() | ![]() Title: Crystal structure of unligated guanylate kinase from yeast reveals GMP-induced conformational changes. Authors: Blaszczyk, J. / Li, Y. / Yan, H. / Ji, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93 KB | Display | ![]() |
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PDB format | ![]() | 70.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.3 KB | Display | ![]() |
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Full document | ![]() | 442.5 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 31.9 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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Unit cell |
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Components
#1: Protein | Mass: 20533.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PET17B / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 39.9 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, Tris-HCl, acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 100 K / pH: 7 Details: drop consists of equal amounts of protein and reservoir solutions | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 24, 1998 / Details: MIRROR |
Radiation | Monochromator: SILICON 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 15759 / Num. obs: 15759 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.37 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9917 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 2.13 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 1.5845 / Num. unique all: 776 / % possible all: 97.9 |
Reflection | *PLUS Num. measured all: 37285 |
Reflection shell | *PLUS % possible obs: 97.9 % |
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Processing
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Refinement | Method to determine structure: HGMAD / Resolution: 2.3→20 Å / Num. parameters: 11965 / Num. restraintsaints: 11875 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER Details: Least-squares refinement using the Konnert-Hendrickson conjugate-gradient algorithm
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3306 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.214 / Rfactor obs: 0.164 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |