[English] 日本語
Yorodumi- PDB-2q7d: Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-kinas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q7d | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-kinase (ITPK1) in complex with AMPPNP and Mn2+ | ||||||
Components | Inositol-tetrakisphosphate 1-kinase | ||||||
Keywords | TRANSFERASE / INOSITOL / INOSITOL KINASE / KINASE / ITPK1 / INOSITOL 1 / 3 / 4-5/6-KINASE / PHOSPHATE / INOSITOL PHOSPHATE / INOSITOLPHOSPHATE / POLYPHOSPHATE | ||||||
Function / homology | Function and homology information inositol-3,4,6-trisphosphate 1-kinase activity / inositol-tetrakisphosphate 1-kinase / inositol-1,3,4-trisphosphate 5/6-kinase / inositol-3,4,5,6-tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol trisphosphate metabolic process / Synthesis of pyrophosphates in the cytosol / neural tube development ...inositol-3,4,6-trisphosphate 1-kinase activity / inositol-tetrakisphosphate 1-kinase / inositol-1,3,4-trisphosphate 5/6-kinase / inositol-3,4,5,6-tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol trisphosphate metabolic process / Synthesis of pyrophosphates in the cytosol / neural tube development / Synthesis of IP3 and IP4 in the cytosol / necroptotic process / catalytic activity / isomerase activity / blood coagulation / Factors involved in megakaryocyte development and platelet production / hydrolase activity / apical plasma membrane / magnesium ion binding / signal transduction / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Chamberlain, P.P. / Lesley, S.A. / Spraggon, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Integration of inositol phosphate signaling pathways via human ITPK1. Authors: Chamberlain, P.P. / Qian, X. / Stiles, A.R. / Cho, J. / Jones, D.H. / Lesley, S.A. / Grabau, E.A. / Shears, S.B. / Spraggon, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2q7d.cif.gz | 172.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2q7d.ent.gz | 133.2 KB | Display | PDB format |
PDBx/mmJSON format | 2q7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q7d_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2q7d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2q7d_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 2q7d_validation.cif.gz | 52.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/2q7d ftp://data.pdbj.org/pub/pdb/validation_reports/q7/2q7d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
| ||||||||
Details | MONOMER ESTABLISHED BY SIZE EXCLUSION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING |
-Components
#1: Protein | Mass: 39031.348 Da / Num. of mol.: 2 / Fragment: Catalytic Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITPK1 / Plasmid: MH4 / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 References: UniProt: Q13572, inositol-tetrakisphosphate 1-kinase, inositol-1,3,4-trisphosphate 5/6-kinase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.76 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1M Na Citrate, 0.2M K/Na Tartrate, 2M (NH4)2SO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 |
---|---|
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 95421 / Num. obs: 95421 / % possible obs: 91.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Selenomethionine derivative partially refined structure Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.279 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.038 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|