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Yorodumi- PDB-1w77: 2C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w77 | ||||||
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Title | 2C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Arabidopsis thaliana | ||||||
Components | 2C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / PLANTHERBICIDE / CYTIDYLYLTRANSFERASE / ARABIDOPSIS THALIANA / NON-MEVALONATE PATHWAY / ISOPRENOID | ||||||
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: 2 Å | ||||||
Authors | Gabrielsen, M. / Kaiser, J. / Rohdich, F. / Eisenreich, W. / Bacher, A. / Bond, C.S. / Hunter, W.N. | ||||||
Citation | 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 | 1w77.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w77.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 1w77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w77_validation.pdf.gz | 708 KB | Display | wwPDB validaton report |
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Full document | 1w77_full_validation.pdf.gz | 768 KB | Display | |
Data in XML | 1w77_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 1w77_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/1w77 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/1w77 | HTTPS FTP |
-Related structure data
Related structure data | 1i52S S: Starting model for refinement |
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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
#1: Protein | Mass: 25500.311 Da / Num. of mol.: 1 / Fragment: CYTIDYLTRANSFERASE DOMAIN, RESIDUES 76-302 / Mutation: YES Source method: isolated from a genetically manipulated source Details: CHLOROPLAST TARGETING SEQUENCE REMOVED, COMPOUND STARTS AT RESIDUE 75 Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PNCO113 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15(PREP4) References: UniProt: O64726, UniProt: P69834*PLUS, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | ||||||
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#2: Chemical | ChemComp-CD / | ||||||
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-C5P / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Details: 0.1 M HEPES PH 7.5, 0.05 M CADMIUM SULFATE, 1 M SODIUM ACETATE, 0.04 COPPER(II) CHLORIDE |
-Data collection
Diffraction | Mean temperature: 160 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 26, 2003 / Details: MIRRORS |
Radiation | Monochromator: SI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.75 Å / Num. obs: 16508 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 16.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.8 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I52 Resolution: 2→27.95 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.875 / SU B: 7.459 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.244 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2→27.95 Å
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Refine LS restraints |
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