+Open data
-Basic information
Entry | Database: PDB / ID: 1jy8 | ||||||
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Title | 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) | ||||||
Components | 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / isoprenoid biosynthesis / terpenes / malaria / drug design | ||||||
Function / homology | Function and homology information 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / ubiquinone biosynthetic process / manganese ion binding / zinc ion binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.5 Å | ||||||
Authors | Steinbacher, S. / Kaiser, J. / Wungsintaweekul, J. / Hecht, S. / Eisenreich, W. / Gerhardt, S. / Bacher, A. / Rohdich, F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of isoprenoids. Authors: Steinbacher, S. / Kaiser, J. / Wungsintaweekul, J. / Hecht, S. / Eisenreich, W. / Gerhardt, S. / Bacher, A. / Rohdich, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jy8.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jy8.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jy8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jy8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1jy8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1jy8_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1jy8_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/1jy8 ftp://data.pdbj.org/pub/pdb/validation_reports/jy/1jy8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Trimer, Symmetry operators: x,y,z y,z,x z,x,y |
-Components
#1: Protein | Mass: 16920.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P62617 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-C5P / |
#4: Chemical | ChemComp-CDI / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2 M Na-formate, 0.1 M HEPES/ NaOH, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 2, 2001 / Details: Osmic mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. all: 17106 / Num. obs: 17106 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.409 / Num. unique all: 2522 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 66701 |
Reflection shell | *PLUS % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→8 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.1 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.201 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.1 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.328 / Rfactor Rwork: 0.291 |