+Open data
-Basic information
Entry | Database: PDB / ID: 2yc5 | ||||||
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Title | Inhibitors of the herbicidal target IspD | ||||||
Components | 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC | ||||||
Keywords | TRANSFERASE / NON-MEVALONATE-PATHWAY / HERBICIDE / ALLOSTERIC POCKET | ||||||
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: 1.6 Å | ||||||
Authors | Hoeffken, H.W. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2011 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: Journal: FEBS J. / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yc5.cif.gz | 117.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yc5.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yc5_validation.pdf.gz | 793 KB | Display | wwPDB validaton report |
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Full document | 2yc5_full_validation.pdf.gz | 797 KB | Display | |
Data in XML | 2yc5_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 2yc5_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/2yc5 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/2yc5 | HTTPS FTP |
-Related structure data
Related structure data | 2yc3SC 2ycmC 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: RESIDUES 76-302 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PNCO113 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / Variant (production host): PREP4 References: UniProt: P69834, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase |
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-Non-polymers , 8 types, 174 molecules
#2: Chemical | ChemComp-6BC / | ||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-MG / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-NA / | #8: Chemical | ChemComp-ZN / | #9: Water | ChemComp-HOH / | |
-Details
Sequence details | RESIDUES 1-61 IN UNIPROT REFERENCE P69834 ARE A CHLOROPLAS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.47 % / 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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→26.1 Å / Num. obs: 31753 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.21 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.59 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YC3 Resolution: 1.6→26.11 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.729 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.079 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.157 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→26.11 Å
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Refine LS restraints |
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