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Yorodumi- PDB-1lrl: Crystal Structure of UDP-Galactose 4-Epimerase Mutant Y299C Compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lrl | ||||||
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Title | Crystal Structure of UDP-Galactose 4-Epimerase Mutant Y299C Complexed with UDP-Glucose | ||||||
Components | UDP-glucose 4-epimerase | ||||||
Keywords | ISOMERASE / epimerase / short chain dehydrogenase / galactosemia | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Thoden, J.B. / Henderson, J.M. / Fridovich-Keil, J.L. / Holden, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structural analysis of the Y299C mutant of Escherichia coli UDP-galactose 4-epimerase. Teaching an old dog new tricks. Authors: Thoden, J.B. / Henderson, J.M. / Fridovich-Keil, J.L. / 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 | 1lrl.cif.gz | 93.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lrl.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lrl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lrl_validation.pdf.gz | 608.6 KB | Display | wwPDB validaton report |
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Full document | 1lrl_full_validation.pdf.gz | 621.1 KB | Display | |
Data in XML | 1lrl_validation.xml.gz | 21 KB | Display | |
Data in CIF | 1lrl_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/1lrl ftp://data.pdbj.org/pub/pdb/validation_reports/lr/1lrl | HTTPS FTP |
-Related structure data
Related structure data | 1lrjC 1lrkC 1ek6S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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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Details | The biological assembly is a homodimer. There is one independent monomer in the unit cell sitting on a crystallographic 2-fold axis. The matrix to generate the second subunit is: 1 0 0 0 -1 0 0 0 -1 0.0 0.0 36.5 |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37233.984 Da / Num. of mol.: 1 / Mutation: Y299C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GALE / Plasmid: pTZSynE / Production host: Escherichia coli (E. coli) / Variant (production host): Bl21(DE3)pLysS / References: UniProt: P09147, UDP-glucose 4-epimerase |
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-Non-polymers , 5 types, 397 molecules
#2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-UPG / | #5: Chemical | ChemComp-PGE / | #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: 2.94 Å3/Da / Density % sol: 58.12 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, HEPPS, NaCl, UDP-glucose, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 115 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 21, 2002 / Details: Supper Mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 39438 / Num. obs: 39438 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.054 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 4523 / Rsym value: 0.337 / % possible all: 82.5 |
Reflection | *PLUS Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 82.5 % / Num. unique obs: 4523 / Rmerge(I) obs: 0.337 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1EK6 Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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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: 35935 / Rfactor all: 0.195 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.194 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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