+Open data
-Basic information
Entry | Database: PDB / ID: 1kvr | ||||||
---|---|---|---|---|---|---|---|
Title | UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH UDP-PHENOL | ||||||
Components | UDP-GALACTOSE 4-EPIMERASE | ||||||
Keywords | ISOMERASE / UDP-GALACTOSE / EPIMERASE / GALACTOSE METABOLISM | ||||||
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: 1.9 Å | ||||||
Authors | Thoden, J.B. / Gulick, A.M. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Molecular structures of the S124A, S124T, and S124V site-directed mutants of UDP-galactose 4-epimerase from Escherichia coli. Authors: Thoden, J.B. / Gulick, A.M. / Holden, H.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kvr.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kvr.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kvr_validation.pdf.gz | 542.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1kvr_full_validation.pdf.gz | 553.3 KB | Display | |
Data in XML | 1kvr_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 1kvr_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kvr ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kvr | 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: 37292.043 Da / Num. of mol.: 1 / Mutation: S124A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P09147, UDP-glucose 4-epimerase |
---|
-Non-polymers , 6 types, 540 molecules
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-UDP / | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.93 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 9 / Details: pH 9.0 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 87 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 32462 / % possible obs: 93 % / Rmerge(I) obs: 0.035 |
Reflection | *PLUS Num. measured all: 59499 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / % possible obs: 85 % / Num. unique obs: 4196 / Num. measured obs: 6546 / Rmerge(I) obs: 0.197 |
-Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.9→30 Å / Details: TNT /
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.179 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|