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Yorodumi- PDB-5kx6: The structure of Arabidopsis thaliana FUT1 Mutant R284K in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kx6 | ||||||
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Title | The structure of Arabidopsis thaliana FUT1 Mutant R284K in complex with GDP | ||||||
Components | Galactoside 2-alpha-L-fucosyltransferase | ||||||
Keywords | CELL ADHESION / acetyl transferase / GT37 | ||||||
Function / homology | Function and homology information galactoside 2-alpha-L-fucosyltransferase activity / xyloglucan biosynthetic process / fucosyltransferase activity / cell wall biogenesis / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi medial cisterna / Golgi cisterna membrane / cell wall organization / Golgi membrane / Golgi apparatus / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Alahuhta, P.M. / Lunin, V.V. | ||||||
Citation | Journal: Plant J. / Year: 2017 Title: Structural, mutagenic and in silico studies of xyloglucan fucosylation in Arabidopsis thaliana suggest a water-mediated mechanism. Authors: Urbanowicz, B.R. / Bharadwaj, V.S. / Alahuhta, M. / Pena, M.J. / Lunin, V.V. / Bomble, Y.J. / Wang, S. / Yang, J.Y. / Tuomivaara, S.T. / Himmel, M.E. / Moremen, K.W. / York, W.S. / Crowley, M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kx6.cif.gz | 385.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kx6.ent.gz | 310.8 KB | Display | PDB format |
PDBx/mmJSON format | 5kx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kx6_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5kx6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5kx6_validation.xml.gz | 41 KB | Display | |
Data in CIF | 5kx6_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/5kx6 ftp://data.pdbj.org/pub/pdb/validation_reports/kx/5kx6 | HTTPS FTP |
-Related structure data
Related structure data | 5koeSC 5kwkC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54195.473 Da / Num. of mol.: 2 / Fragment: residues 84-558 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FUT1, FT1, MUR2, At2g03220, T18E12.11 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q9SWH5, EC: 2.4.1.69 |
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-Non-polymers , 5 types, 615 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-MES / | #6: 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: 2.4 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 7 mg/mL protein in 0.1 M MES pH 6.0 to 7.0 and 16% to 23% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Aug 5, 2015 / Details: Helios mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→85.03 Å / Num. obs: 47518 / % possible obs: 91.2 % / Redundancy: 2.71 % / Rmerge(I) obs: 0.1077 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.4809 / Mean I/σ(I) obs: 1.14 / % possible all: 84.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KOE Resolution: 2.2→85.03 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.844 / SU B: 28.604 / SU ML: 0.337 / Cross valid method: THROUGHOUT / ESU R: 0.451 / ESU R Free: 0.317 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.028 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→85.03 Å
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Refine LS restraints |
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