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Yorodumi- PDB-1udc: STRUCTURE OF UDP-GALACTOSE-4-EPIMERASE COMPLEXED WITH UDP-MANNOSE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1udc | |||||||||
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Title | STRUCTURE OF UDP-GALACTOSE-4-EPIMERASE COMPLEXED WITH UDP-MANNOSE | |||||||||
Components | UDP-GALACTOSE-4-EPIMERASE | |||||||||
Keywords | ISOMERASE / UDP-GALACTOSE / EPIMERASE | |||||||||
Function / homology | Function and homology information colanic acid biosynthetic process / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / racemase and epimerase activity, acting on carbohydrates and derivatives / galactose catabolic process via UDP-galactose / galactose metabolic process / NAD+ binding / carbohydrate metabolic process / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.65 Å | |||||||||
Authors | Thoden, J.B. / Holden, H.M. | |||||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Structural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coli. Authors: Thoden, J.B. / Hegeman, A.D. / Wesenberg, G. / Chapeau, M.C. / Frey, P.A. / 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 | 1udc.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1udc.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 1udc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/1udc ftp://data.pdbj.org/pub/pdb/validation_reports/ud/1udc | HTTPS FTP |
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-Related 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37308.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P09147, UDP-glucose 4-epimerase |
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-Non-polymers , 6 types, 568 molecules
#2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-UFM / | #5: Chemical | ChemComp-PGE / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.1 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 9 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 50521 / % possible obs: 95 % / Redundancy: 3.17 % |
Reflection shell | Resolution: 1.65→1.73 Å / Rmerge(I) obs: 0.182 / % possible all: 89 |
Reflection | *PLUS Highest resolution: 1.65 Å / Num. measured all: 160336 / Rmerge(I) obs: 0.033 |
Reflection shell | *PLUS % possible obs: 89 % / Num. unique obs: 5849 / Num. measured obs: 11518 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.65→30 Å / Rfactor Rwork: 0.177 Details: SET OF IDEAL BOND LENGTHS AND ANGLES OTHER THAN ENGH AND HUBER USED DURING REFINEMENT | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→30 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 50521 / Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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