+Open data
-Basic information
Entry | Database: PDB / ID: 5mrm | ||||||
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Title | Arabidopsis thaliana IspD in complex with Isoxazole (4) | ||||||
Components | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic | ||||||
Keywords | TRANSFERASE / herbicide / anti-infectives / drug discovery / allosteric inhibition | ||||||
Function / homology | Function and homology information 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 | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Schwab, A. / Illarionov, B. / Frank, A. / Kunfermann, A. / Seet, M. / Bacher, A. / Witschel, M. / Fischer, M. / Groll, M. / Diederich, F. | ||||||
Funding support | Germany, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mrm.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mrm.ent.gz | 84.8 KB | Display | PDB format |
PDBx/mmJSON format | 5mrm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mrm_validation.pdf.gz | 816.8 KB | Display | wwPDB validaton report |
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Full document | 5mrm_full_validation.pdf.gz | 819 KB | Display | |
Data in XML | 5mrm_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 5mrm_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/5mrm ftp://data.pdbj.org/pub/pdb/validation_reports/mr/5mrm | HTTPS FTP |
-Related structure data
Related structure data | 5mrnC 5mroC 5mrpC 5mrqC 4nakS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 25430.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: truncated mutant (delta 1-74 / R149S) / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ISPD, MCT, MECT, MEPCT, At2g02500, T8K22.20 / Production host: Escherichia coli (E. coli) References: UniProt: P69834, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase |
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-Non-polymers , 6 types, 142 molecules
#2: Chemical | ChemComp-Q9T / | ||||
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#3: Chemical | ChemComp-TRS / | ||||
#4: Chemical | ChemComp-ACT / | ||||
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.02 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 15, 2015 |
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: 22217 / % possible obs: 99.2 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.9 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NAK Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.963 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.127 / 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: 58.805 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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