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Yorodumi- PDB-1uda: STRUCTURE OF UDP-GALACTOSE-4-EPIMERASE COMPLEXED WITH UDP-4-DEOXY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uda | ||||||
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Title | STRUCTURE OF UDP-GALACTOSE-4-EPIMERASE COMPLEXED WITH UDP-4-DEOXY-4-FLUORO-ALPHA-D-GALACTOSE | ||||||
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: 1.8 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 | 1uda.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uda.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 1uda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uda_validation.pdf.gz | 562.1 KB | Display | wwPDB validaton report |
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Full document | 1uda_full_validation.pdf.gz | 577.5 KB | Display | |
Data in XML | 1uda_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 1uda_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/1uda ftp://data.pdbj.org/pub/pdb/validation_reports/ud/1uda | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 |
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-Non-polymers , 6 types, 565 molecules
#2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-UFG / | #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-EDO / | #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: 58.12 % | ||||||||||||||||||||||||
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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: 39033 / % possible obs: 92 % / Redundancy: 3.09 % / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 1.8→1.88 Å / Rmerge(I) obs: 0.216 / % possible all: 83 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. measured all: 120477 |
Reflection shell | *PLUS % possible obs: 83 % / Num. unique obs: 4283 / Num. measured obs: 9159 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→30 Å / Rfactor Rwork: 0.188 Details: SET OF IDEAL BOND LENGTHS AND ANGLES OTHER THAN ENGH AND HUBER USED DURING REFINEMENT | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 39033 / Rfactor obs: 0.188 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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