+
Open data
-
Basic information
Entry | Database: PDB / ID: 8e1i | ||||||
---|---|---|---|---|---|---|---|
Title | Asp1 kinase in complex with ATP Mg 5-IP7 | ||||||
![]() | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase | ||||||
![]() | TRANSFERASE / Inositol pyrophosphosphate IPP kinase Fission yeast | ||||||
Function / homology | ![]() regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity / regulation of mitotic spindle elongation (spindle phase three) / Synthesis of pyrophosphates in the cytosol / diphosphoinositol-pentakisphosphate 1-kinase / inositol heptakisphosphate kinase activity / diphosphoinositol-pentakisphosphate kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity ...regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity / regulation of mitotic spindle elongation (spindle phase three) / Synthesis of pyrophosphates in the cytosol / diphosphoinositol-pentakisphosphate 1-kinase / inositol heptakisphosphate kinase activity / diphosphoinositol-pentakisphosphate kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / inositol hexakisphosphate kinase activity / inositol phosphate catabolic process / inositol phosphate metabolic process / signaling / inositol phosphate biosynthetic process / intracellular phosphate ion homeostasis / inositol metabolic process / mitotic spindle assembly / regulation of microtubule cytoskeleton organization / 2 iron, 2 sulfur cluster binding / cytoskeleton / phosphorylation / ATP hydrolysis activity / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Goldgur, Y. / Shuman, S. / Benjamin, B. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structures of Fission Yeast Inositol Pyrophosphate Kinase Asp1 in Ligand-Free, Substrate-Bound, and Product-Bound States. Authors: Benjamin, B. / Goldgur, Y. / Jork, N. / Jessen, H.J. / Schwer, B. / Shuman, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 157.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 119.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 29.5 KB | Display | |
Data in CIF | ![]() | 43.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8e1hSC ![]() 8e1jC ![]() 8e1sC ![]() 8e1tC ![]() 8e1vC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38213.652 Da / Num. of mol.: 2 / Mutation: K47A, R50A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: asp1, vip1, SPCC1672.06c / Production host: ![]() ![]() References: UniProt: O74429, diphosphoinositol-pentakisphosphate 1-kinase #2: Chemical | ChemComp-I7P / ( | #3: Chemical | ChemComp-ATP / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.45 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.05 M bis-tris propane (pH 7.8), 0.1 M NaF, and 20% PEG 3,350 Temp details: ambient |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 S 1M / Detector: PIXEL / Date: Jul 31, 2022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 93269 / % possible obs: 98.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 34.39 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.031 / Rrim(I) all: 0.067 / Χ2: 1.615 / Net I/σ(I): 13.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 8E1H Resolution: 2→36.67 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.23 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.31 Å2 / Biso mean: 39.1681 Å2 / Biso min: 21.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→36.67 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
|