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- PDB-1ex7: CRYSTAL STRUCTURE OF YEAST GUANYLATE KINASE IN COMPLEX WITH GUANO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ex7 | ||||||
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Title | CRYSTAL STRUCTURE OF YEAST GUANYLATE KINASE IN COMPLEX WITH GUANOSINE-5'-MONOPHOSPHATE | ||||||
![]() | GUANYLATE KINASE | ||||||
![]() | TRANSFERASE / GUANYLATE KINASE / SUBSTRATE-INDUCED FIT / DOMAIN MOVEMENT / GMP / ATP / SUBSTRATE SPECIFICITY | ||||||
Function / homology | ![]() Azathioprine ADME / GDP biosynthetic process / guanylate kinase / purine nucleotide metabolic process / Interconversion of nucleotide di- and triphosphates / guanylate kinase activity / ATP binding / nucleus / cytosol / cytoplasm 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 | ![]() | 56 KB | Display | ![]() |
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PDB format | ![]() | 39.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ex6C ![]() 1gkyS S: Starting model for refinement C: citing same article ( |
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Similar 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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PET17B / Species (production host): Escherichia coli / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-5GP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: ammonium sulfate, sodium phosphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Dec 5, 1996 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. all: 15836 / Num. obs: 15836 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 1.8455 / Num. unique all: 716 / % possible all: 86.9 |
Reflection | *PLUS Num. measured all: 72765 |
Reflection shell | *PLUS % possible obs: 86.9 % |
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Processing
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Refinement | Method to determine structure: REFINEMENT OF THE MODEL Starting model: 1GKY Resolution: 1.9→15 Å / Num. parameters: 6733 / Num. restraintsaints: 6051 / 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: 1688 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.1701 / Rfactor obs: 0.156 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |