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Yorodumi- PDB-3ukk: Crystal structure of R182K-UDP-galactopuranose mutase from Asperg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ukk | ||||||
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Title | Crystal structure of R182K-UDP-galactopuranose mutase from Aspergillus fumigatus in complex with UDPgalp | ||||||
Components | UDP-galactopyranose mutase | ||||||
Keywords | ISOMERASE / FLAVOENZYME / FAD / FADH2 ISOMERASE | ||||||
Function / homology | Function and homology information UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Aspergillus fumigatus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Van Straaten, K.E. / Sanders, D.A.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural Insight into the Unique Substrate Binding Mechanism and Flavin Redox State of UDP-galactopyranose Mutase from Aspergillus fumigatus. Authors: van Straaten, K.E. / Routier, F.H. / 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 | 3ukk.cif.gz | 418.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ukk.ent.gz | 342 KB | Display | PDB format |
PDBx/mmJSON format | 3ukk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/3ukk ftp://data.pdbj.org/pub/pdb/validation_reports/uk/3ukk | HTTPS FTP |
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-Related structure data
Related structure data | 3ukaC 3ukfC 3ukhC 3uklC 3ukpC 3ukqC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 57871.305 Da / Num. of mol.: 4 / Mutation: R182K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: CSB 144-89 / Gene: glf, glfA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: Q4W1X2, UDP-galactopyranose mutase #2: Chemical | #3: Chemical | ChemComp-UDP / #4: Chemical | ChemComp-FAD / | #5: 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: 2.87 Å3/Da / Density % sol: 57.18 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 8.5 Details: 0.1M Bis-Tris-Propane pH 7.5-8.5, 0.2-0.35M sodium citrate, 10-20% PEG 3350, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97934 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 16, 2011 / Details: collimating mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→48.1 Å / Num. all: 173167 / Num. obs: 67309 / % possible obs: 93.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 7.66 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: reduced AfUGM:UDPgalp complex Resolution: 2.75→47.987 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.76 / Isotropic thermal model: Isotropic / σ(F): 1.99 / Phase error: 23.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.07 Å2 / ksol: 0.345 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.75→47.987 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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