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- PDB-1r6d: Crystal Structure of DesIV double mutant (dTDP-glucose 4,6-dehydr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r6d | ||||||
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Title | Crystal Structure of DesIV double mutant (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and DAU bound | ||||||
![]() | TDP-glucose-4,6-dehydratase | ||||||
![]() | LYASE / Dehydratase / Rossmann Fold / Short-Chain Dehydrogenase/Reductase | ||||||
Function / homology | ![]() dTDP-glucose 4,6-dehydratase / UDP-L-rhamnose synthase activity / UDP-glucose 4,6-dehydratase activity / UDP-rhamnose biosynthetic process / dTDP-glucose 4,6-dehydratase activity / flavonol biosynthetic process / oxidoreductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Allard, S.T.M. / Cleland, W.W. / Holden, H.M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.9 KB | Display | ![]() |
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PDB format | ![]() | 64.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r66SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The biological assembly is a dimer, contructed from chain A (a symmetry partner generated by the two-fold). |
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Components
#1: Protein | Mass: 36497.918 Da / Num. of mol.: 1 / Mutation: D128N/E129Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-DAU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: batch macro-seeding / pH: 6.5 Details: Peg 8000, magnesium chloride, cacodylate, pH 6.5, Batch macro-seeding, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Aug 13, 2003 / Details: Gobel focusing optics |
Radiation | Monochromator: GOEBEL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. all: 61664 / Num. obs: 61664 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Redundancy: 3.6 % / Rsym value: 0.04 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.35→1.41 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 6573 / Rsym value: 0.223 / % possible all: 81 |
Reflection | *PLUS Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 81 % / Num. unique obs: 6573 / Rmerge(I) obs: 0.223 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R66 Resolution: 1.35→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.35→30 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 55477 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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