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Open data
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Basic information
Entry | Database: PDB / ID: 6xi2 | ||||||
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Title | Apo form of POMGNT2 | ||||||
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Function / homology | ![]() protein O-mannose beta-1,4-N-acetylglucosaminyltransferase / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Halmo, S.M. / Yeh, J. / Wells, L. / Moremen, K.W. / Lanzilotta, W.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of beta-1,4-N-acetylglucosaminyltransferase 2: structural basis for inherited muscular dystrophies. Authors: Yang, J.Y. / Halmo, S.M. / Praissman, J. / Chapla, D. / Singh, D. / Wells, L. / Moremen, K.W. / Lanzilotta, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 432.2 KB | Display | ![]() |
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PDB format | ![]() | 355.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase ... , 4 types, 4 molecules ABDC
#1: Protein | Mass: 61017.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8NAT1, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase |
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#2: Protein | Mass: 60240.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8NAT1, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase |
#3: Protein | Mass: 60972.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8NAT1, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase |
#4: Protein | Mass: 60143.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8NAT1, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase |
-Protein/peptide , 2 types, 2 molecules GH
#5: Protein/peptide | Mass: 728.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#6: Protein/peptide | Mass: 700.741 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Sugars , 1 types, 3 molecules ![](data/chem/img/NAG.gif)
#7: Sugar | ![]() |
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-Non-polymers , 2 types, 173 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-PO4 / ![]() #9: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.29 Å3/Da / Density % sol: 71.32 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M potassium/sodium tartrate, 0.1 M Bis-Tris, pH 7.9, 10% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 13, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.57→50 Å / Num. obs: 131723 / % possible obs: 99.1 % / Redundancy: 14.6 % / CC1/2: 0.864 / CC star: 0.963 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.57→2.66 Å / Num. unique obs: 12111 / CC1/2: 0.864 / CC star: 0.963 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.08 Å2 / Biso mean: 48.964 Å2 / Biso min: 21.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.57→45.99 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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