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- PDB-5mro: Arabidopsis thaliana IspD Glu258Ala mutant in complex with Azolop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mro | ||||||
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Title | Arabidopsis thaliana IspD Glu258Ala mutant in complex with Azolopyrimidine (1) | ||||||
![]() | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic | ||||||
![]() | TRANSFERASE / herbicide / anti-infectives / drug discovery / allosteric inhibition / mutant | ||||||
Function / homology | ![]() 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / chloroplast stroma / chloroplast Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schwab, A. / Illarionov, B. / Frank, A. / Kunfermann, A. / Seet, M. / Bacher, A. / Witschel, M. / Fischer, M. / Groll, M. / Diederich, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of Allosteric Inhibition of the Enzyme IspD by Three Different Classes of Ligands. Authors: Schwab, A. / Illarionov, B. / Frank, A. / Kunfermann, A. / Seet, M. / Bacher, A. / Witschel, M.C. / Fischer, M. / Groll, M. / 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 | ![]() | 110 KB | Display | ![]() |
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PDB format | ![]() | 83.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 817.3 KB | Display | ![]() |
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Full document | ![]() | 817.9 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mrmC ![]() 5mrnC ![]() 5mrpC ![]() 5mrqC ![]() 2yc5S 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25372.158 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Truncated mutant (delta 1-74 / R149S) Glu258Ala-Mutant Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P69834, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase |
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-Non-polymers , 6 types, 141 molecules ![](data/chem/img/Q9P.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-Q9P / | ||
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#3: Chemical | ChemComp-TRS / | ||
#4: Chemical | ChemComp-ACT / | ||
#5: Chemical | ChemComp-K / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50 mM HEPES, 50 mM CdSO4, 800 mM KAc |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 22644 / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 5.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2YC5 Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.445 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.689 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→15 Å
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Refine LS restraints |
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