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Open data
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Basic information
Entry | Database: PDB / ID: 2ycm | ||||||
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Title | Inhibitors of herbicidal target IspD | ||||||
![]() | 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC | ||||||
![]() | TRANSFERASE / HERBICIDE / ALLOSTERIC BINDING POCKET / NON-MEVALONATE-PATHWAY | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Hoeffken, H.W. | ||||||
![]() | ![]() Title: Inhibitors of the Herbicidal Target Ispd: Allosteric Site Binding. Authors: Witschel, M.C. / Hoeffken, H.W. / Seet, M. / Parra, L. / Mietzner, T. / Thater, F. / Niggeweg, R. / Rohl, F. / Illarionov, B. / Rohdich, F. / Kaiser, J. / Fischer, M. / Bacher, A. / Diederich, F. #1: ![]() Title: The Crystal Structure of a Plant 2C-Methyl-D- Erythritol 4-Phosphate Cytidylyltransferase Exhibits a Distinct Quaternary Structure Compared to Bacterial Homologues and a Possible Role in ...Title: The Crystal Structure of a Plant 2C-Methyl-D- Erythritol 4-Phosphate Cytidylyltransferase Exhibits a Distinct Quaternary Structure Compared to Bacterial Homologues and a Possible Role in Feedback Regulation for Cytidine Monophosphate. Authors: Gabrielsen, M. / Kaiser, J. / Rohdich, F. / Eisenreich, W. / Laupitz, R. / Bacher, A. / Bond, C.S. / Hunter, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.5 KB | Display | ![]() |
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PDB format | ![]() | 79.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 772.1 KB | Display | ![]() |
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Full document | ![]() | 776.3 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yc3SC ![]() 2yc5C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25299.000 Da / Num. of mol.: 1 / Fragment: CYTIDYLTRANSFERASE DOMAIN, RESIDUES 76-302 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P69834, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase |
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-Non-polymers , 5 types, 99 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/30A.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/30A.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CU / | #5: Chemical | ChemComp-30A / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.48 % / Description: NONE |
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Crystal grow | Details: NATIVE CRYSTALS (SEE REMARK 1, PDB 1W77) WERE SOAKED WITH A SATURATED SOLUTION OF LIGAND |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 16, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939272 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→36.5 Å / Num. obs: 22629 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.84 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 2.43 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YC3 Resolution: 1.8→73.61 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.984 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE ELECTRON DENSITY MAP SUGGESTS THAT IN THE CRYSTAL THE ALLOSTERIC POCKET IS ONLY PARTIALLY OCCUPIED AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE ELECTRON DENSITY MAP SUGGESTS THAT IN THE CRYSTAL THE ALLOSTERIC POCKET IS ONLY PARTIALLY OCCUPIED AND THEREFOR THE ELECTRON DENSITY REFLECTS AN OVERLAY OF THE UNLIGANDED AND LIGANDED ENZYME. THIS IS IN ACCORDANCE WITH THE HIGH TEMPERATURE FACTORS OF PART THE LIGAND AND OF THE AMINO ACIDS 264 TO 268 WHICH HAVE TO MOVE TO OPEN THE ALLOSTERIC BINDING POCKET.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.227 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→73.61 Å
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