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Yorodumi- PDB-3hdy: Crystal Structure of UDP-galactopyranose mutase (reduced form) in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hdy | ||||||
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Title | Crystal Structure of UDP-galactopyranose mutase (reduced form) in complex with substrate | ||||||
Components | UDP-galactopyranose mutase | ||||||
Keywords | ISOMERASE / UDP-galactopyranose mutase / reduced form / substrate | ||||||
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 | 3hdy.cif.gz | 752.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hdy.ent.gz | 622.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hdy_validation.pdf.gz | 6.8 MB | Display | wwPDB validaton report |
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Full document | 3hdy_full_validation.pdf.gz | 7 MB | Display | |
Data in XML | 3hdy_validation.xml.gz | 143.6 KB | Display | |
Data in CIF | 3hdy_validation.cif.gz | 179.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/3hdy ftp://data.pdbj.org/pub/pdb/validation_reports/hd/3hdy | HTTPS FTP |
-Related structure data
Related structure data | 3hdqC 3he3C 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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Details | 5 homodimers |
-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, DR_AO367 / Plasmid: pEHISTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: Q9RYF1, UDP-galactopyranose mutase #2: Chemical | ChemComp-GDU / #3: Chemical | ChemComp-FAD / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.53 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 6.5 Details: 0.1 M HEPES pH 6.5, 0.2 M LiCl and 28 % PEG 6000, Microbatch, temperature 295K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9797 Å |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2009 |
Radiation | 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→39.94 Å / Num. obs: 189435 / % possible obs: 95.8 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Redundancy: 4.7 % / Rmerge(I) obs: 0.187 / Rsym value: 0.187 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.34 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 1.7 / Num. unique all: 78255 / % possible all: 92.1 |
-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→39.94 Å / SU ML: -0 / σ(F): 1.34 / Phase error: 30.92 / 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: 66.28 Å2 / ksol: 0.393 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→39.94 Å
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Refine LS restraints |
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LS refinement shell |
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