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Yorodumi- PDB-1tvm: NMR structure of enzyme GatB of the galactitol-specific phosphoen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tvm | ||||||
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Title | NMR structure of enzyme GatB of the galactitol-specific phosphoenolpyruvate-dependent phosphotransferase system | ||||||
Components | PTS system, galactitol-specific IIB component | ||||||
Keywords | TRANSFERASE / phosphotransferase system (PTS) / P-loop / four-stranded parallel open twisted beta sheet flanked by alpha helices on both sides / E. coli / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics | ||||||
Function / homology | Function and homology information protein-Npi-phosphohistidine-galactitol phosphotransferase / galactitol metabolic process / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Volpon, L. / Young, C.R. / Lim, N.S. / Iannuzzi, P. / Cygler, M. / Gehring, K. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: NMR structure of the enzyme GatB of the galactitol-specific phosphoenolpyruvate-dependent phosphotransferase system and its interaction with GatA. Authors: Volpon, L. / Young, C.R. / Matte, A. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tvm.cif.gz | 681 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tvm.ent.gz | 567.9 KB | Display | PDB format |
PDBx/mmJSON format | 1tvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tvm_validation.pdf.gz | 345.8 KB | Display | wwPDB validaton report |
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Full document | 1tvm_full_validation.pdf.gz | 537.7 KB | Display | |
Data in XML | 1tvm_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 1tvm_validation.cif.gz | 68.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/1tvm ftp://data.pdbj.org/pub/pdb/validation_reports/tv/1tvm | 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: 12481.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GATB, C2618, Z3256, ECS2896, SF2155, S2281 / Plasmid: pHIVTEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q8X7H5, UniProt: P0A435*PLUS, protein-Npi-phosphohistidine-sugar phosphotransferase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear and 3D heteronuclear techniques. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 100 mM Phosphate, 75 mM NaCl, 75 mM KCl / pH: 6.8 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: the structures are based on a total of 1377 restraints: 1119 NOE-derived distance constraints, 120 dihedral angle restraints, 56 distance restraints from hydrogen bonds (28 hydrogen bonds), ...Details: the structures are based on a total of 1377 restraints: 1119 NOE-derived distance constraints, 120 dihedral angle restraints, 56 distance restraints from hydrogen bonds (28 hydrogen bonds), and 82 15N-1H residual dipolar couplings. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |