+Open data
-Basic information
Entry | Database: PDB / ID: 4nan | ||||||
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Title | Arabidopsis thaliana IspD in complex with tetrabromo-pseudilin | ||||||
Components | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / herbicide / anti-infectives / pseudilin / natural product / drug discovery / allosteric inhibition / Rossmann Fold / Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 | Kunfermann, A. / Witschel, M. / Illarionov, B. / Martin, R. / Rottmann, M. / Hoffken, H.W. / Seet, M. / Eisenreich, W. / Knolker, H.-J. / Fischer, M. ...Kunfermann, A. / Witschel, M. / Illarionov, B. / Martin, R. / Rottmann, M. / Hoffken, H.W. / Seet, M. / Eisenreich, W. / Knolker, H.-J. / Fischer, M. / Bacher, A. / Groll, M. / Diederich, F. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Pseudilins: Halogenated, Allosteric Inhibitors of the Non-Mevalonate Pathway Enzyme IspD. Authors: Kunfermann, A. / Witschel, M. / Illarionov, B. / Martin, R. / Rottmann, M. / Hoffken, H.W. / Seet, M. / Eisenreich, W. / Knolker, H.J. / Fischer, M. / Bacher, A. / 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 | 4nan.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nan.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nan.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nan_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4nan_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4nan_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 4nan_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/4nan ftp://data.pdbj.org/pub/pdb/validation_reports/na/4nan | HTTPS FTP |
-Related structure data
Related structure data | 4naiSC 4nakC 4nalC 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 / Fragment: UNP residues 76-302 / Mutation: R149S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g02500, ISPD, MCT, MECT, MEPCT, T8K22.20 / Plasmid: pNCO113 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 References: UniProt: P69834, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase |
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-Non-polymers , 6 types, 94 molecules
#2: Chemical | ChemComp-2JM / | ||||||
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#3: Chemical | ChemComp-DTT / | ||||||
#4: Chemical | ChemComp-CD / #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-CL / | #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: 2.39 Å3/Da / Density % sol: 48.6 % |
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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, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2013 |
Radiation | Monochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 22879 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 3.6 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4NAI Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.622 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.539 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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