[English] 日本語
Yorodumi- PDB-1udb: STRUCTURE OF UDP-GALACTOSE-4-EPIMERASE COMPLEXED WITH UDP-4-DEOXY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1udb | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF UDP-GALACTOSE-4-EPIMERASE COMPLEXED WITH UDP-4-DEOXY-4-FLUORO-ALPHA-D-GLUCOSE | ||||||
Components | UDP-GALACTOSE-4-EPIMERASE | ||||||
Keywords | ISOMERASE / UDP-GALACTOSE / EPIMERASE | ||||||
Function / homology | Function and homology information 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 | 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1udb.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1udb.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 1udb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1udb_validation.pdf.gz | 558.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1udb_full_validation.pdf.gz | 568.4 KB | Display | |
Data in XML | 1udb_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 1udb_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/1udb ftp://data.pdbj.org/pub/pdb/validation_reports/ud/1udb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37294.016 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 |
---|
-Non-polymers , 6 types, 582 molecules
#2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-UFG / | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.12 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 9 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 49619 / % possible obs: 93 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.051 |
Reflection shell | Resolution: 1.65→1.73 Å / Rmerge(I) obs: 0.23 / % possible all: 81 |
Reflection | *PLUS Highest resolution: 1.65 Å / Num. measured all: 124280 |
Reflection shell | *PLUS % possible obs: 81 % / Num. unique obs: 5317 / Num. measured obs: 8489 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.65→30 Å / Rfactor Rwork: 0.179 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
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 49616 / Rfactor obs: 0.179 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.012 |