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Yorodumi- PDB-2n6d: NMR structure of the 140-315 fragment of the N-acetylglucosamine-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2n6d | ||||||
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Title | NMR structure of the 140-315 fragment of the N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits | ||||||
Components | N-acetylglucosamine-1-phosphotransferase subunits alpha/beta | ||||||
Keywords | TRANSFERASE / PSI-Biology / N-acetylglucosamine-1-phosphate transferase / Structural Genomics / Joint Center for Structural Genomics / JCSG | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase / N-glycan processing to lysosome / secretion of lysosomal enzymes / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / carbohydrate phosphorylation / lysosome organization / Golgi membrane / calcium ion binding / Golgi apparatus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be Published Title: NMR structure of the 140-315 fragment of the N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits Authors: Serrano, P. / Wuthrich, K. / Geralt, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n6d.cif.gz | 1003.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n6d.ent.gz | 840.4 KB | Display | PDB format |
PDBx/mmJSON format | 2n6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2n6d_validation.pdf.gz | 472.2 KB | Display | wwPDB validaton report |
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Full document | 2n6d_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2n6d_validation.xml.gz | 222.9 KB | Display | |
Data in CIF | 2n6d_validation.cif.gz | 165.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/2n6d ftp://data.pdbj.org/pub/pdb/validation_reports/n6/2n6d | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 19155.080 Da / Num. of mol.: 1 / Fragment: UNP residues 135-305 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNPTAB, GNPTA, KIAA1208 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q3T906 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.2 mM [U-98% 13C; U-98% 15N] protein, 50 mM sodium chloride, 20 mM sodium phosphate, 5 mM sodium azide, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.24 / pH: 6 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: CYANA / Developer: Guntert, P. et al. / Classification: refinement |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: SEMI-AUTOMATED STRUCTURE DETERMINATION WITH THE J-UNIO SUITE |
NMR constraints | NOE constraints total: 2126 / NOE intraresidue total count: 616 / NOE long range total count: 525 / NOE medium range total count: 305 / NOE sequential total count: 680 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 80 / Conformers submitted total number: 19 |