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- PDB-2amt: Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2amt | ||||||
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Title | Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase complexed with a CDP derived fluorescent inhibitor | ||||||
![]() | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ||||||
![]() | LYASE / ISOPRENOID / ISOPRENE 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 | ![]() ![]() ![]() | ||||||
![]() | Ramsden, N.L. / Hunter, W.N. | ||||||
![]() | ![]() Title: Fluorescent Inhibitors for IspF, an Enzyme in the Non-Mevalonate Pathway for Isoprenoid Biosynthesis and a Potential Target for Antimalarial Therapy. Authors: Crane, C.M. / Kaiser, J. / Ramsden, N.L. / Lauw, S. / Rohdich, F. / Eisenreich, W. / Hunter, W.N. / Bacher, A. / Diederich, 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 | ![]() | 194 KB | Display | ![]() |
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PDB format | ![]() | 153.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 40.8 KB | Display | |
Data in CIF | ![]() | 53.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gzlC ![]() 1gx1S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16920.531 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P62617, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-1AA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 53.81 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M ammonium sulfate, 10% PEG 200 MME, 0.1M sodium acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 6, 2004 / Details: mirror |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.5 Å / Num. all: 47682 / Num. obs: 47420 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.9 / Redundancy: 3.5 % / Biso Wilson estimate: 29.85 Å2 / Rsym value: 0.097 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 3.9 / Num. unique all: 6904 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GX1 Resolution: 2.3→29.5 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.881 / SU B: 9.344 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.618 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.42 Å / Total num. of bins used: 20
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