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Yorodumi- PDB-1ek5: STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH NAD+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ek5 | ||||||
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Title | STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH NAD+ | ||||||
Components | UDP-GALACTOSE 4-EPIMERASE | ||||||
Keywords | ISOMERASE / Short-Chain Dehydrogenase / Epimerase / Galactosemia | ||||||
Function / homology | Function and homology information Defective GALE causes EDG / UDP-N-acetylglucosamine 4-epimerase / UDP-N-acetylglucosamine 4-epimerase activity / galactose catabolic process / Galactose catabolism / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Thoden, J.B. / Wohlers, T.M. / Fridovich-Keil, J.L. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase. Authors: Thoden, J.B. / Wohlers, T.M. / Fridovich-Keil, J.L. / 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 | 1ek5.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ek5.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ek5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ek5_validation.pdf.gz | 768.8 KB | Display | wwPDB validaton report |
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Full document | 1ek5_full_validation.pdf.gz | 778.9 KB | Display | |
Data in XML | 1ek5_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 1ek5_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/1ek5 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/1ek5 | HTTPS FTP |
-Related structure data
-Links
-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 constructed from a symmetry partner generated by the two-fold. |
-Components
#1: Protein | Mass: 38324.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: FORESKIN / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q14376, UDP-glucose 4-epimerase |
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#2: Chemical | ChemComp-NAD / |
#3: 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: 2.49 Å3/Da / Density % sol: 50.59 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG-8000, KCl, HEPPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: May 27, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 34184 / Num. obs: 34184 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.258 / Num. unique all: 3761 / % possible all: 87 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 87 % / Num. unique obs: 3761 / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Resolution: 1.8→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor all: 0.191 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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