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Open data
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Basic information
Entry | Database: PDB / ID: 1jkf | ||||||
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Title | Holo 1L-myo-inositol-1-phosphate Synthase | ||||||
![]() | myo-inositol-1-phosphate synthase | ||||||
![]() | ISOMERASE / Rossmann Fold | ||||||
Function / homology | ![]() Synthesis of IP2, IP, and Ins in the cytosol / inositol-3-phosphate synthase / inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stein, A.J. / Geiger, J.H. | ||||||
![]() | ![]() Title: The crystal structure and mechanism of 1-L-myo-inositol- 1-phosphate synthase Authors: Stein, A.J. / Geiger, J.H. #1: ![]() Title: Structural Studies of MIP Synthase Authors: Stein, A.J. / Geiger, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.5 KB | Display | ![]() |
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PDB format | ![]() | 167.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 547.2 KB | Display | ![]() |
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Full document | ![]() | 632.2 KB | Display | |
Data in XML | ![]() | 32.7 KB | Display | |
Data in CIF | ![]() | 48.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The biological assembly is a tetramer. The tetramer has 222 symmetry with a non-crystallographic 2-fold axis relating the dimer in the asymmetric unit and a crystallographic 2-fold axis relating the two dimers that make up the tetramer. The assymmetric unit operations are x, y, z and -x, y, -z. |
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Components
#1: Protein | Mass: 59707.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.65 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG 8000, sodium acetate, water, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: J., Stein. A., (2000) Acta Crystallogr., Sect.D, 56, 348. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Detector: CCD / Date: Mar 28, 2000 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→500 Å / Num. all: 91546 / Num. obs: 49388 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.85 % / Rsym value: 0.048 / Net I/σ(I): 12.6 | ||||||||||||
Reflection shell | Resolution: 2.4→2.5 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.338 / % possible all: 92.6 | ||||||||||||
Reflection | *PLUS Lowest resolution: 500 Å / Num. measured all: 91546 / Rmerge(I) obs: 0.048 | ||||||||||||
Reflection shell | *PLUS % possible obs: 92.6 % / Rmerge(I) obs: 0.338 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.42 Å /
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Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor all: 0.207 / Rfactor obs: 0.205 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.205 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.0095 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.268 |