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- PDB-2gzl: 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: 2gzl | |||||||||
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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 | ![]() ![]() ![]() | |||||||||
![]() | Crane, C.M. / Kaiser, J. / Ramsden, N.L. / Lauw, S. / Rohdich, F. / Wolfgang, E. / Hunter, W.N. / Bacher, A. / Diederich, F. | |||||||||
![]() | ![]() 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 | ![]() | 49.1 KB | Display | ![]() |
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PDB format | ![]() | 32.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1006.2 KB | Display | ![]() |
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Full document | ![]() | 1019 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2amtC ![]() 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16932.520 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-ZN / |
#3: Chemical | ChemComp-2AA / |
#4: Chemical | ChemComp-GPP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.7 Å3/Da / Density % sol: 81.65 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M AMMONIUM SULFATE, 8% PEG 200 MME, 0.1M SODIUM ACETATE, pH 5.00, 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: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→28.5 Å / Num. obs: 17715 / % possible obs: 99.8 % / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.685 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GX1 Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.041 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.162 / 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: 51.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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