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- PDB-1lrk: Crystal Structure of Escherichia coli UDP-Galactose 4-Epimerase M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lrk | |||||||||
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Title | Crystal Structure of Escherichia coli UDP-Galactose 4-Epimerase Mutant Y299C Complexed with UDP-N-acetylglucosamine | |||||||||
![]() | UDP-glucose 4-epimerase | |||||||||
![]() | ISOMERASE / epimerase / short chain dehydrogenase / galactosemia | |||||||||
Function / homology | ![]() colanic acid biosynthetic process / racemase and epimerase activity, acting on carbohydrates and derivatives / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / galactose metabolic process / NAD+ binding / carbohydrate metabolic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Thoden, J.B. / Henderson, J.M. / Fridovich-Keil, J.L. / Holden, H.M. | |||||||||
![]() | ![]() Title: Structural analysis of the Y299C mutant of Escherichia coli UDP-galactose 4-epimerase. Teaching an old dog new tricks. Authors: Thoden, J.B. / Henderson, J.M. / Fridovich-Keil, J.L. / 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 | ![]() | 98 KB | Display | ![]() |
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PDB format | ![]() | 72.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lrjC ![]() 1lrlC ![]() 1ek6S C: citing same article ( S: Starting model for refinement |
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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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Components on special symmetry positions |
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Details | The biological assembly is a homodimer. One independent monomer in the unit cell sits on a crystallographic 2-fold axis. The matrix to generate the second subunit of the dimer is: 1 0 0 0 -1 0 0 0 -1 0.0 0.0 36.5 |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37233.984 Da / Num. of mol.: 1 / Mutation: Y299C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 550 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/UD1.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/UD1.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-UD1 / | #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.75 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, NaCl, HEPES, UDP-N-acetylglucosamine, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 115 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 22, 2002 / Details: Supper Mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 44201 / Num. obs: 44201 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.055 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.75→1.83 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 5325 / Rsym value: 0.312 / % possible all: 83 |
Reflection | *PLUS Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 83 % / Num. unique obs: 5325 / Rmerge(I) obs: 0.312 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1EK6 Resolution: 1.75→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 40001 / Rfactor all: 0.174 / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.171 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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