+Open data
-Basic information
Entry | Database: PDB / ID: 2ffv | ||||||
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Title | Human ppGalNAcT-2 complexed with manganese and UDP | ||||||
Components | Polypeptide N-acetylgalactosaminyltransferase 2 | ||||||
Keywords | TRANSFERASE / ppGalNAcT / mucin / glycosyltransferase | ||||||
Function / homology | Function and homology information protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / Golgi cisterna membrane ...protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / Golgi cisterna membrane / protein maturation / manganese ion binding / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Fritz, T.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Dynamic Association between the Catalytic and Lectin Domains of Human UDP-GalNAc:Polypeptide {alpha}-N-Acetylgalactosaminyltransferase-2 Authors: Fritz, T.A. / Raman, J. / Tabak, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ffv.cif.gz | 206.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ffv.ent.gz | 162.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ffv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ffv_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2ffv_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2ffv_validation.xml.gz | 39 KB | Display | |
Data in CIF | 2ffv_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/2ffv ftp://data.pdbj.org/pub/pdb/validation_reports/ff/2ffv | HTTPS FTP |
-Related structure data
Related structure data | 2ffuC 1xhbS S: Starting model for refinement 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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3 |
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Unit cell |
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Details | The biological assembly is either one of the two monomers |
-Components
#1: Protein | Mass: 57129.844 Da / Num. of mol.: 2 / Fragment: Catalytic and lectin domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: Invitrogen pPIC9 vector with TEV-protease-cleavable, N-terminal engineered 6His tag Gene: GALNT2 / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1168 References: UniProt: Q10471, polypeptide N-acetylgalactosaminyltransferase #2: Chemical | #3: Chemical | |
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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: 2.83 Å3/Da / Density % sol: 56.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG, Hepes, MnCl2, EDTA, mercaptoethanol, UDP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97472 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 2, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97472 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→49.1 Å / Num. all: 34646 / Num. obs: 34265 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 64.6 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Separate catalytic domains of PDB entry 1XHB in which nonconserved residues were changed to alanine Resolution: 2.75→49.1 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2290873.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.276 Å2 / ksol: 0.334354 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→49.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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