[English] 日本語
![](img/lk-miru.gif)
- PDB-5a7j: Crystal structure of INPP5B in complex with benzene 1,2,4,5- tetr... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5a7j | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of INPP5B in complex with benzene 1,2,4,5- tetrakisphosphate | |||||||||
![]() | TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5-PHOSPHATASE | |||||||||
![]() | HYDROLASE / SGC / SIGNALLING / STRUCTURAL GENOMICS CONSORTIUM STOCKHOLM / MAGNESIUM BINDING / PROTEIN-INHBITOR COMPLEX / INHIBITOR / PHOSPHOINOSITIDES SIGNALLING | |||||||||
Function / homology | ![]() Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / flagellated sperm motility / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of protein processing / Synthesis of IP3 and IP4 in the cytosol ...Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / flagellated sperm motility / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of protein processing / Synthesis of IP3 and IP4 in the cytosol / endoplasmic reticulum-Golgi intermediate compartment / phagocytic vesicle membrane / early endosome membrane / spermatogenesis / in utero embryonic development / Golgi apparatus / signal transduction / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tresaugues, L. / Mills, S.J. / Silvander, C. / Cozier, G. / Potter, B.V.L. / Nordlund, P. | |||||||||
![]() | ![]() Title: Crystal Structures of Type-II Inositol Polyphosphate 5-Phosphatase Inpp5B with Synthetic Inositol Polyphosphate Surrogates Reveal New Mechanistic Insights for the Inositol 5-Phosphatase Family. Authors: Mills, S.J. / Silvander, C. / Cozier, G. / Tresaugues, L. / Nordlund, P. / Potter, B.V.L. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 259.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 213.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 33.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a7iC ![]() 3n9vS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.72408, 0.00399, -0.68971), Vector: |
-
Components
#1: Protein | Mass: 36201.086 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 339-643 Source method: isolated from a genetically manipulated source Details: CLONED WITH A C-TERMINAL HEXAHISTIDINE TAG / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.89 % / Description: NONE |
---|---|
Crystal grow | pH: 5.5 Details: 0.2 M LI2SO4, 0.1 M BIS-TRIS PH 5.5 AND 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→48.48 Å / Num. obs: 16223 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 52.88 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3N9V Resolution: 2.9→48.48 Å / Cor.coef. Fo:Fc: 0.9009 / Cor.coef. Fo:Fc free: 0.8422 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: REMARK 3 NULL
| ||||||||||||||||||||
Displacement parameters | Biso mean: 39.21 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→48.48 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.1 Å / Total num. of bins used: 8
|