+Open data
-Basic information
Entry | Database: PDB / ID: 1kvs | |||||||||
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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 / 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: 2.15 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kvs.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kvs.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kvs ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kvs | 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: 37308.039 Da / Num. of mol.: 1 / Mutation: S124T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P09147, UDP-glucose 4-epimerase |
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-Non-polymers , 5 types, 422 molecules
#2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-UPG / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.91 % | ||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9.0 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 87 K |
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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: 2.15→30 Å / Num. obs: 24177 / % possible obs: 95 % / Rmerge(I) obs: 0.064 |
Reflection | *PLUS Num. measured all: 68358 |
Reflection shell | *PLUS Highest resolution: 2.15 Å / % possible obs: 87 % / Num. unique obs: 3002 / Num. measured obs: 5614 / Rmerge(I) obs: 0.245 |
-Processing
Software |
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Refinement | Resolution: 2.15→30 Å / Details: TNT /
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Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.188 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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