+Open data
-Basic information
Entry | Database: PDB / ID: 1jkf | ||||||
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Title | Holo 1L-myo-inositol-1-phosphate Synthase | ||||||
Components | myo-inositol-1-phosphate synthase | ||||||
Keywords | ISOMERASE / Rossmann Fold | ||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Stein, A.J. / Geiger, J.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: The crystal structure and mechanism of 1-L-myo-inositol- 1-phosphate synthase Authors: Stein, A.J. / Geiger, J.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structural Studies of MIP Synthase Authors: Stein, A.J. / Geiger, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jkf.cif.gz | 202.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jkf.ent.gz | 167.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/1jkf ftp://data.pdbj.org/pub/pdb/validation_reports/jk/1jkf | HTTPS FTP |
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-Related structure data
-Links
-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. |
-Components
#1: Protein | Mass: 59707.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P11986, inositol-3-phosphate synthase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9796, 0.9464 | ||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→10 Å / σ(F): 2 / Stereochemistry target values: CNS, Terwilliger
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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 |