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Yorodumi- PDB-1r66: Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from St... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r66 | ||||||
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Title | Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and TYD bound | ||||||
Components | TDP-glucose-4,6-dehydratase | ||||||
Keywords | LYASE / Dehydratase / Rossmann Fold / Short-Chain Dehydrogenase/Reductase | ||||||
Function / homology | Function and homology information dTDP-glucose 4,6-dehydratase / UDP-L-rhamnose synthase activity / UDP-glucose 4,6-dehydratase activity / UDP-rhamnose biosynthetic process / flavonol biosynthetic process / dTDP-glucose 4,6-dehydratase activity / auxin export across the plasma membrane / oxidoreductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Streptomyces venezuelae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | ||||||
Authors | Allard, S.T.M. / Cleland, W.W. / Holden, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: High Resolution X-ray Structure of dTDP-Glucose 4,6-Dehydratase from Streptomyces venezuelae Authors: Allard, S.T.M. / Cleland, W.W. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r66.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r66.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 1r66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r66_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1r66_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1r66_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 1r66_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/1r66 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/1r66 | HTTPS FTP |
-Related structure data
Related structure data | 1r6dC 1bxkS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36499.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: DesIV / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)PLysS / References: UniProt: Q9ZGH3, dTDP-glucose 4,6-dehydratase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-NAD / |
#4: Chemical | ChemComp-TYD / |
#5: 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 Å3/Da / Density % sol: 38.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: batch / pH: 6.3 Details: PEG 8000, magnesium acetate tetrahydrate, sodium cacodylate, pH 6.3, Batch, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 94 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Dec 4, 2002 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→50 Å / Num. all: 57828 / Num. obs: 56518 / % possible obs: 98.6 % / Redundancy: 5.5 % / Rsym value: 0.066 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.44→1.49 Å / Redundancy: 4 % / Mean I/σ(I) obs: 6.8 / Num. unique all: 5618 / Rsym value: 0.212 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 1.44 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 99.9 % / Num. unique obs: 5618 / Rmerge(I) obs: 0.212 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BXK Resolution: 1.44→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: Used weighted least squares procedure.
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Refinement step | Cycle: LAST / Resolution: 1.44→30 Å
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Refine LS restraints |
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Software | *PLUS Version: 'V. 5-E' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 52099 / Rfactor obs: 0.177 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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