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Open data
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Basic information
Entry | Database: PDB / ID: 1u3l | ||||||
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Title | IspF with Mg and CDP | ||||||
![]() | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ||||||
![]() | LYASE / MEP pathway / terpene biosynthesis | ||||||
Function / homology | ![]() 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / ubiquinone biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / manganese ion binding / zinc ion binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Steinbacher, S. / Kaiser, J. / Wungsintaweekul, J. / Hechst, S. / Eisenreich, W. / Gerhardt, S. / Bacher, A. / Rohdich, F. | ||||||
![]() | ![]() 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. / Hechst, S. / Eisenreich, W. / Gerhardt, S. / Bacher, A. / Rohdich, 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 | ![]() | 43.4 KB | Display | ![]() |
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PDB format | ![]() | 29.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 779.2 KB | Display | ![]() |
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Full document | ![]() | 782.1 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 10.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jy8SC ![]() 1u3pC ![]() 1u40C ![]() 1u43C S: Starting model for refinement C: citing same article ( |
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Similar 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 | Trimer generated by crystallographic three-fold x,y,z y,z,x z,x,y |
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Components
#1: Protein | Mass: 16920.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P62617, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-CDP / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.45 Å3/Da / Density % sol: 84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: ammonium formiate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. all: 17015 / Num. obs: 17015 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.064 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JY8 Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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