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Yorodumi- PDB-1vsq: Solution NMR structure of the productive complex between IIAManno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vsq | ||||||
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Title | Solution NMR structure of the productive complex between IIAMannose and IIBMannose of the mannose transporter of the E. coli phosphotransferase system | ||||||
Components |
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Keywords | TRANSFERASE / phosphotransferase / sugar transport / transferase-phosphocarrier complex / Membrane / Phosphoprotein / Phosphotransferase system | ||||||
Function / homology | Function and homology information protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation / protein homodimerization activity / membrane ...protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation / protein homodimerization activity / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / conjoined rigid body, torsion angle simulated annealing | ||||||
Authors | Clore, G.M. / Hu, J. / Hu, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Solution NMR Structures of Productive and Non-productive Complexes between the A and B Domains of the Cytoplasmic Subunit of the Mannose Transporter of the Escherichia coli Phosphotransferase System. Authors: Hu, J. / Hu, K. / Williams, D.C. / Komlosh, M.E. / Cai, M. / Clore, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vsq.cif.gz | 296.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vsq.ent.gz | 246 KB | Display | PDB format |
PDBx/mmJSON format | 1vsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/1vsq ftp://data.pdbj.org/pub/pdb/validation_reports/vs/1vsq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14527.425 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: manX, gptB, ptsL / Plasmid: pET32a modified / Production host: Escherichia coli (E. coli) References: UniProt: P69797, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Protein | | Mass: 18332.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: manX, gptB, ptsL / Plasmid: pET32a modified / Production host: Escherichia coli (E. coli) References: UniProt: P69797, protein-Npi-phosphohistidine-sugar phosphotransferase Compound details | MODEL 1 IS PHOSPHORYLATED-HIS IN CHAIN B OF IIAMAN. MODEL 2 IS A PHOSPHORYL TRANSITION STATE ...MODEL 1 IS PHOSPHORYL | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: Triple resonance experiments for assignment. Quantitative J correlation experiments for heteronuclear scalar couplings. 3D and 2D isotope filtered/isotope-separated NOE experiments for intermolecular NOEs. |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 20 mM phosphate / pH: 6.5 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: conjoined rigid body, torsion angle simulated annealing Software ordinal: 2 Details: COORDINATES OF IIAMAN (1PDO) AND IIBMAN (2JZH) ARE TREATED AS RIGID BODIES WITH THE INTERFACIAL SIDE CHAINS GIVEN TORSIONAL DEGREES OF FREEDOM. RESIDUES 130- 134 OF IIAMAN ARE ALSO GIVEN ...Details: COORDINATES OF IIAMAN (1PDO) AND IIBMAN (2JZH) ARE TREATED AS RIGID BODIES WITH THE INTERFACIAL SIDE CHAINS GIVEN TORSIONAL DEGREES OF FREEDOM. RESIDUES 130- 134 OF IIAMAN ARE ALSO GIVEN TORSIONAL DEGREES OF FREEDOM SINCE INTERMOLECULAR NOES WERE OBSERVED INVOLVED THESE RESIDUES ALTHOUGH THEY ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP OF THE X-RAY STRUCTURE OF FREE IIAMAN. FURTHER DETAILS IN PUBLICATION. THE COORDINATES of 1VSQ ARE DERIVED DIRECTLY FROM THOSE OF 2JZN, THE IIAMAN(H10E)-IIBMAN COMPLEX. | ||||||||||||
NMR ensemble | Conformer selection criteria: restrained regularized mean / Conformers calculated total number: 120 / Conformers submitted total number: 2 | ||||||||||||
NMR ensemble rms | Distance rms dev: 0.02 Å |