[English] 日本語
Yorodumi- PDB-1awb: HUMAN MYO-INOSITOL MONOPHOSPHATASE IN COMPLEX WITH D-INOSITOL-1-P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1awb | ||||||
---|---|---|---|---|---|---|---|
Title | HUMAN MYO-INOSITOL MONOPHOSPHATASE IN COMPLEX WITH D-INOSITOL-1-PHOSPHATE AND CALCIUM | ||||||
Components | MYO-INOSITOL MONOPHOSPHATASE | ||||||
Keywords | HYDROLASE / MYO-INOSITOL / PHOSPHATASE | ||||||
Function / homology | Function and homology information D-galactose 1-phosphate phosphatase / inositol monophosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / lithium ion binding / inositol biosynthetic process / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process ...D-galactose 1-phosphate phosphatase / inositol monophosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / lithium ion binding / inositol biosynthetic process / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process / phosphatidylinositol biosynthetic process / phosphate-containing compound metabolic process / phosphatidylinositol phosphate biosynthetic process / manganese ion binding / magnesium ion binding / signal transduction / protein homodimerization activity / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Rondeau, J.-M. / Pelton, P.D. / Vincendon, P. / Ganzhorn, A.J. | ||||||
Citation | Journal: Protein Eng. / Year: 1997 Title: Structure of an Enzyme-Substrate Complex and the Catalytic Mechanism of Human Brain Myo-Inositol Monophosphatase Authors: Ganzhorn, A.J. / Rondeau, J.-M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1awb.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1awb.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 1awb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1awb_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1awb_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | 1awb_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 1awb_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/1awb ftp://data.pdbj.org/pub/pdb/validation_reports/aw/1awb | HTTPS FTP |
-Related structure data
Related structure data | 2hhmS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.995599, -0.093643, -0.003701), Vector: |
-Components
#1: Protein | Mass: 30088.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: IMPA / Organ: BRAIN / Plasmid: BL21 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P29218, inositol-phosphate phosphatase #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % |
---|---|
Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 18% PEG 8,000, 100MM SODIUM CACODYLATE PH 6.5, 200MM CALCIUM ACETATE, 1MM EDTA, 4MM DTT, 40MM D-INOSITOL-1-PHOSPHATE, 0.1M SODIUM CACODYLATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 273 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1993 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. obs: 20214 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.073 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.243 / % possible all: 79.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HHM Resolution: 2.5→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|