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- PDB-1dk4: CRYSTAL STRUCTURE OF MJ0109 GENE PRODUCT INOSITOL MONOPHOSPHATASE -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dk4 | ||||||
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Title | CRYSTAL STRUCTURE OF MJ0109 GENE PRODUCT INOSITOL MONOPHOSPHATASE | ||||||
![]() | INOSITOL MONOPHOSPHATASE | ||||||
![]() | HYDROLASE / HOMODIMER / COMPLEXED WITH ZN AND PI | ||||||
Function / homology | ![]() inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / phosphatidylinositol phosphate biosynthetic process / signal transduction / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Stec, B. / Yang, H. / Johnson, K.A. / Chen, L. / Roberts, M.F. | ||||||
![]() | ![]() Title: MJ0109 is an enzyme that is both an inositol monophosphatase and the 'missing' archaeal fructose-1,6-bisphosphatase. Authors: Stec, B. / Yang, H. / Johnson, K.A. / Chen, L. / Roberts, M.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.7 KB | Display | ![]() |
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PDB format | ![]() | 88.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 412.9 KB | Display | ![]() |
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Full document | ![]() | 451.1 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1awbS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a dimer constructed from chain 1 and 2 both present in the asssymetric unit |
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Components
#1: Protein | Mass: 28611.838 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PET23A(+) / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG 8000, calcium chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: UCSD MARK II / Detector: AREA DETECTOR / Date: Jul 14, 1998 / Details: graphite |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 21885 / Num. obs: 21539 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.6→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.1 / Num. unique all: 4222 / % possible all: 96.1 |
Reflection | *PLUS % possible obs: 98.3 % / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS Lowest resolution: 2.7 Å / % possible obs: 95.5 % / Rmerge(I) obs: 0.41 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1awb Resolution: 2.6→12 Å / Num. parameters: 16427 / Num. restraintsaints: 16868 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: SHELXL conjugent gradient
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Solvent computation | Solvent model: moews & kretsinger | |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4036 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→12 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / σ(F): 4 / % reflection Rfree: 4 % / Rfactor obs: 0.186 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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