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Yorodumi- PDB-5gy7: X-Ray structure of H243I mutant of UDP-Galactose 4-epimerase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gy7 | ||||||
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Title | X-Ray structure of H243I mutant of UDP-Galactose 4-epimerase from E.coli:evidence for existence of open and closed active site during catalysis. | ||||||
Components | UDP-glucose 4-epimerase | ||||||
Keywords | ISOMERASE / Induced fit mechanism | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Singh, N. / Tiwari, P. / Phulera, S. / Dixit, A. / Choudhury, D. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: X-Ray structure of H243I mutant of UDP-Galactose 4-epimerase from E.coli:evidence for existence of open and closed active site during catalysis. Authors: Singh, N. / Tiwari, P. / Phulera, S. / Dixit, A. / Choudhury, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gy7.cif.gz | 161.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gy7.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 5gy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gy7_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5gy7_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5gy7_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 5gy7_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/5gy7 ftp://data.pdbj.org/pub/pdb/validation_reports/gy/5gy7 | HTTPS FTP |
-Related structure data
Related structure data | 1xelS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38111.922 Da / Num. of mol.: 2 / Mutation: H243I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: galE, galD, b0759, JW0742 / Variant: W3110 / Plasmid: PET22b+ / 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, 650 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-NO3 / | #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: 2.08 Å3/Da / Density % sol: 40.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Ammonium Nitrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→79.07 Å / Num. obs: 121857 / % possible obs: 98.7 % / Redundancy: 3.3 % / Net I/σ(I): 7.73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XEL Resolution: 1.43→79.07 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.729 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.625 Å2
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Refinement step | Cycle: 1 / Resolution: 1.43→79.07 Å
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Refine LS restraints |
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