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Yorodumi- PDB-1r7t: Glycosyltransferase A in complex with 3-deoxy-acceptor analog inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r7t | |||||||||
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Title | Glycosyltransferase A in complex with 3-deoxy-acceptor analog inhibitor | |||||||||
Components | Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase | |||||||||
Keywords | TRANSFERASE / Glycoprotein / transmembrane / signal-anchor / blood group antigen | |||||||||
Function / homology | Function and homology information fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | |||||||||
Authors | Nguyen, H.P. / Seto, N.O.L. / Cai, Y. / Leinala, E.K. / Borisova, S.N. / Palcic, M.M. / Evans, S.V. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The influence of an intramolecular hydrogen bond in differential recognition of inhibitory acceptor analogs by human ABO(H) blood group A and B glycosyltransferases Authors: Nguyen, H.P. / Seto, N.O.L. / Cai, Y. / Leinala, E.K. / Borisova, S.N. / Palcic, M.M. / Evans, S.V. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallography & NMR System Authors: Brunger, A.T. / Adams, P.D. / Clore, G.M. / Delano, W.L. / Gros, P. / Grosse-Kunstleve, R. / Jiang, J.-S. / Kuszewski, J. / Nilges, M. / Pannu, N.S. / Read, R.J. / Rice, L.M. / Simonson, T. / Warren, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r7t.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r7t.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 1r7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r7t_validation.pdf.gz | 657.9 KB | Display | wwPDB validaton report |
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Full document | 1r7t_full_validation.pdf.gz | 663.3 KB | Display | |
Data in XML | 1r7t_validation.xml.gz | 14 KB | Display | |
Data in CIF | 1r7t_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/1r7t ftp://data.pdbj.org/pub/pdb/validation_reports/r7/1r7t | HTTPS FTP |
-Related structure data
Related structure data | 1r7uC 1r7vC 1r7xC 1r7yC 1r80C 1r81C 1r82C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32999.148 Da / Num. of mol.: 1 / Fragment: Catalytic Domain (Residues 63-345) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase | ||
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#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-hexyl 3-deoxy-beta-D-galactopyranoside Type: oligosaccharide / Mass: 394.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-HG / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 48.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging dropDetails: Patenaude, S.I., (2002) Nat. Struct. Biol., 9, 685. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.15 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→19.95 Å / Num. all: 35232 / Num. obs: 35232 / Observed criterion σ(F): 0 / Biso Wilson estimate: 26.2 Å2 / Limit h max: 24 / Limit h min: 0 / Limit k max: 71 / Limit k min: 0 / Limit l max: 38 / Limit l min: -38 / Observed criterion F max: 1016433.73 / Observed criterion F min: 0.45 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 18777 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 96.4 % / Rmerge(I) obs: 0.379 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→19.95 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 63.2927 Å2 / ksol: 0.415119 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.4 Å2 / Biso mean: 39.21 Å2 / Biso min: 19.13 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.09→19.95 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.214 / Rfactor Rwork: 0.209 |