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- PDB-3kyb: Structure of UDP-galactopyranose mutase bound to flavin mononucleotide -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kyb | ||||||
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Title | Structure of UDP-galactopyranose mutase bound to flavin mononucleotide | ||||||
![]() | Probable UDP-galactopyranose mutase | ||||||
![]() | ISOMERASE / flavoenzyme / protein-ligand complex / carbohydrate biosynthesis / FAD / Flavoprotein / Lipopolysaccharide biosynthesis | ||||||
Function / homology | ![]() UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / O antigen biosynthetic process / flavin adenine dinucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gruber, T.D. / Dimond, M.C. / Kiessling, L.L. / Forest, K.T. | ||||||
![]() | ![]() Title: Structure of UDP-galactopyranose mutase bound to flavin mononucleotide Authors: Gruber, T.D. / Dimond, M.C. / Kiessling, L.L. / Forest, K.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.6 KB | Display | ![]() |
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PDB format | ![]() | 141 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 35.7 KB | Display | |
Data in CIF | ![]() | 49.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gf4S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45237.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-FMN / #4: Water | ChemComp-HOH / | Sequence details | THESE ARE VERY CONSERVATIVE MUTATIONS FROM THE PUBLISHED SEQUENCE. THEY REFLECT SEQUENCE ...THESE ARE VERY CONSERVATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: DROPS CONTAINING 1.5 MICROLITERS 5 MG/ML PROTEIN IN 20 MM HEPES PH 7.0 WERE COMBINED WITH 1.5 MICROLITERS WELL SOLUTION (85 MM AMMONIUM ACETATE, 42 MM TRI-SODIUM CITRATE, 12.3% PEG 4000, 7. ...Details: DROPS CONTAINING 1.5 MICROLITERS 5 MG/ML PROTEIN IN 20 MM HEPES PH 7.0 WERE COMBINED WITH 1.5 MICROLITERS WELL SOLUTION (85 MM AMMONIUM ACETATE, 42 MM TRI-SODIUM CITRATE, 12.3% PEG 4000, 7.5% GLYCEROL, 15 MM L-CYSTEINE, 5 MM UDP-GLC) FOR 1-2 WEEKS. CRYSTAL WAS THEN SOAKED IN A SOLUTION OF 53% QIAGEN CRYOS SUITE CONDITION #87 WITH 15 MM L-CYS AND 23 MM FLAVIN MONONUCLEOTIDE (24HRS). CRYSTAL WAS BRIEFLY SOAKED (20 SECONDS) IN A SOLUTION OF 53% QIAGEN CRYOS SUITE CONDITION #87 WITH 15 MM L-CYS, 30% METHANOL, 10 MM FLAVIN MONONUCLEOTIDE PRIOR TO VITRIFICATION, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2008 / Details: beryllium lens |
Radiation | Monochromator: C(111) diamond laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 49496 / Num. obs: 49472 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 39.2 Å2 / Rsym value: 0.093 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 7.2 / Num. unique all: 4912 / Rsym value: 0.286 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3GF4 Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.245 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.197 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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