+Open data
-Basic information
Entry | Database: PDB / ID: 5cqn | ||||||
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Title | GTB mutant without mercury - E303C | ||||||
Components | Histo-blood group ABO system transferase | ||||||
Keywords | TRANSFERASE / Human ABO(H) blood group system / Glycosyltransferase / Double turn motif / Catalytic domain | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Gagnon, S.M.L. / Blackler, R.J. | ||||||
Citation | Journal: Glycobiology / Year: 2017 Title: Glycosyltransfer in mutants of putative catalytic residue Glu303 of the human ABO(H) A and B blood group glycosyltransferases GTA and GTB proceeds through a labile active site. Authors: Blackler, R.J. / Gagnon, S.M. / Polakowski, R. / Rose, N.L. / Zheng, R.B. / Letts, J.A. / Johal, A.R. / Schuman, B. / Borisova, S.N. / Palcic, M.M. / Evans, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cqn.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cqn.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 5cqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cqn_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 5cqn_full_validation.pdf.gz | 429.4 KB | Display | |
Data in XML | 5cqn_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 5cqn_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/5cqn ftp://data.pdbj.org/pub/pdb/validation_reports/cq/5cqn | HTTPS FTP |
-Related structure data
Related structure data | 5cmfC 5cmgC 5cmhC 5cmiC 5cmjC 5cqlC 5cqmC 5cqoC 5cqpC 1lz0S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34259.586 Da / Num. of mol.: 1 / Fragment: Catalytic domain (UNP residues 64-354) / Mutation: E303C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Production host: Escherichia coli (E. coli) References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase |
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#2: 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: 2.25 Å3/Da / Density % sol: 45.29 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 30-40 mg/ml protein, 1% PEG (w/v) 4000, 4.5% MPD (v/v), 0.1 M ammonium sulfate, 0.07 M NaCl, 0.05 M ADA buffer, pH 7.5, 5 mM MnCl2 against a reservoir containing 2.7% (w/v) PEG 4000, 7% (v/v) ...Details: 30-40 mg/ml protein, 1% PEG (w/v) 4000, 4.5% MPD (v/v), 0.1 M ammonium sulfate, 0.07 M NaCl, 0.05 M ADA buffer, pH 7.5, 5 mM MnCl2 against a reservoir containing 2.7% (w/v) PEG 4000, 7% (v/v) MPD, 0.32 M ammonium sulfate, 0.25 M NaCl, and 0.2 M ADA pH 7.5 |
-Data collection
Diffraction | Mean temperature: 113 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 1, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.61→74.95 Å / Num. obs: 38967 / % possible obs: 96.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.037 / Χ2: 0.96 / Net I/σ(I): 18.5 / Num. measured all: 176577 / Scaling rejects: 1325 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LZ0 Resolution: 1.61→74.95 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.551 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.088 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.92 Å2 / Biso mean: 25.467 Å2 / Biso min: 12.85 Å2
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Refinement step | Cycle: final / Resolution: 1.61→74.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.652 Å / Total num. of bins used: 20
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