+Open data
-Basic information
Entry | Database: PDB / ID: 2c20 | ||||||
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Title | CRYSTAL STRUCTURE OF UDP-GLUCOSE 4-EPIMERASE | ||||||
Components | UDP-GLUCOSE 4-EPIMERASE | ||||||
Keywords | ISOMERASE / CARBOHYDRATE METABOLISM / GALACTOSE METABOLISM / NAD / SPINE | ||||||
Function / homology | Function and homology information UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose metabolic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS ANTHRACIS (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Lebedev, A.A. / Moroz, O.V. / Blagova, E.V. / Levdikov, V.M. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Udp-Glucose 4-Epimerase from Bacillus Anthracis at 2.7A Resolution Authors: Lebedev, A.A. / Moroz, O.V. / Blagova, E.V. / Levdikov, V.M. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c20.cif.gz | 391.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c20.ent.gz | 323.1 KB | Display | PDB format |
PDBx/mmJSON format | 2c20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/2c20 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/2c20 | HTTPS FTP |
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-Related structure data
Related structure data | 1gy8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 36955.531 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q81K34, UniProt: A0A6L8PTV5*PLUS, UDP-glucose 4-epimerase #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY INVOLVES UDP-GLUCOSE = UDP-GALACTOSE. | |
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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: 3 Å3/Da / Density % sol: 58.5 % |
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Crystal grow | pH: 6.5 Details: 22% PEG 2K MME, 0.2M CALCIUM ACETATE, 0.1 MES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.00806 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 25, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00806 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. obs: 70638 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GY8 Resolution: 2.7→25.02 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 39.3 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→25.02 Å
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