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Yorodumi- PDB-3he3: Crystal Structure of UDP-galactopyranose mutase in complex with UDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3he3 | ||||||
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Title | Crystal Structure of UDP-galactopyranose mutase in complex with UDP | ||||||
Components | UDP-galactopyranose mutase | ||||||
Keywords | ISOMERASE / UDP-galactopyranose mutase / inhibitor / UDP | ||||||
Function / homology | Function and homology information UDP-galactopyranose mutase activity / flavin adenine dinucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Partha, S.K. / van Straaten, K.E. / Sanders, D.A.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural basis of substrate binding to UDP-galactopyranose mutase: crystal structures in the reduced and oxidized state complexed with UDP-galactopyranose and UDP. Authors: Partha, S.K. / van Straaten, K.E. / Sanders, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3he3.cif.gz | 771.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3he3.ent.gz | 636.8 KB | Display | PDB format |
PDBx/mmJSON format | 3he3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/3he3 ftp://data.pdbj.org/pub/pdb/validation_reports/he/3he3 | HTTPS FTP |
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-Related structure data
Related structure data | 3hdqC 3hdyC 1v0jS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 45741.824 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: R1 / Gene: DR_A0367 / Plasmid: pEHISTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: Q9RYF1, UDP-galactopyranose mutase #2: Chemical | ChemComp-UDP / #3: Chemical | ChemComp-FAD / #4: 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: 2.89 Å3/Da / Density % sol: 57.42 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 6.5 Details: 0.1 M HEPES, 0.2 M LiCl and 28% PEG 6000, pH 6.5, Microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9797 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2009 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→39.88 Å / Num. obs: 204114 / % possible obs: 98.9 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.182 / Rsym value: 0.182 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.5 / Num. unique all: 66447 / Rsym value: 0.598 / % possible all: 93.1 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1V0J Resolution: 2.4→39.88 Å / SU ML: -0 / σ(F): 1.34 / Phase error: 28.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.776 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→39.88 Å
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Refine LS restraints |
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LS refinement shell |
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