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Yorodumi- PDB-2czk: Crystal structure of human myo-inositol monophosphatase 2 (IMPA2)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2czk | ||||||
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Title | Crystal structure of human myo-inositol monophosphatase 2 (IMPA2) (trigonal form) | ||||||
Components | Inositol monophosphatase 2 | ||||||
Keywords | HYDROLASE / myo-inositol monophosphatase (IMPase) / bipolar disorder / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Synthesis of IP2, IP, and Ins in the cytosol / inositol biosynthetic process / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process / phosphate-containing compound metabolic process / response to lithium ion / phosphatidylinositol phosphate biosynthetic process ...Synthesis of IP2, IP, and Ins in the cytosol / inositol biosynthetic process / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process / phosphate-containing compound metabolic process / response to lithium ion / phosphatidylinositol phosphate biosynthetic process / signal transduction / protein homodimerization activity / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Arai, R. / Ito, K. / Hanawa-Suetsugu, K. / Ohnishi, T. / Ohba, H. / Yoshikawa, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proteins / Year: 2007 Title: Crystal structure of human myo-inositol monophosphatase 2, the product of the putative susceptibility gene for bipolar disorder, schizophrenia, and febrile seizures Authors: Arai, R. / Ito, K. / Ohnishi, T. / Ohba, H. / Akasaka, R. / Bessho, Y. / Hanawa-Suetsugu, K. / Yoshikawa, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2czk.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2czk.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 2czk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/2czk ftp://data.pdbj.org/pub/pdb/validation_reports/cz/2czk | HTTPS FTP |
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-Related structure data
Related structure data | 2czhSC 2cziC 2ddkC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | A dimer between A and A' generated by the operation: x-y+1,-y+2,-z-1/3 |
-Components
#1: Protein | Mass: 32402.014 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IMPA2 / Plasmid: pET44a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O14732, inositol-phosphate phosphatase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.01M Potassium dihydrogen phosphate, 12% PEG 8000, 20% Glycerol, 2mM MgSO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 20, 2004 / Details: Two dimensional focusing mirror |
Radiation | Monochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 9243 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 30.9 Å2 / Rsym value: 0.088 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 661 / Rsym value: 0.496 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CZH Resolution: 2.9→49.44 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 346269.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.8501 Å2 / ksol: 0.332546 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→49.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
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Xplor file |
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