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Yorodumi- PDB-1pzq: Structure of fused docking domains from the erythromycin polyketi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pzq | ||||||
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Title | Structure of fused docking domains from the erythromycin polyketide synthase (DEBS), a model for the interaction between DEBS 2 and DEBS 3: The A domain | ||||||
Components | Erythronolide synthase | ||||||
Keywords | TRANSFERASE / FOUR HELIX BUNDLE / HOMODIMER | ||||||
Function / homology | Function and homology information 6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Saccharopolyspora erythraea (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Broadhurst, R.W. / Nietlispach, D. / Wheatcroft, M.P. / Leadlay, P.F. / Weissman, K.J. | ||||||
Citation | Journal: Chem.Biol. / Year: 2003 Title: The structure of docking domains in modular polyketide synthases. Authors: Broadhurst, R.W. / Nietlispach, D. / Wheatcroft, M.P. / Leadlay, P.F. / Weissman, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pzq.cif.gz | 275.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pzq.ent.gz | 237.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/1pzq ftp://data.pdbj.org/pub/pdb/validation_reports/pz/1pzq | 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: 6428.874 Da / Num. of mol.: 2 / Fragment: C-terminal fragment / Mutation: L1G, F2S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: ERYA / Plasmid: pGEX4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS / Keywords: Insertion of GS at N-terminus References: UniProt: Q03132, 6-deoxyerythronolide-B synthase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. Intermolecular contacts were obtained from an X-filtered NOESY experiment on a mixed-labeled sample. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 100mM phosphate buffer NA / pH: 6.5 / Pressure: ambient / Temperature: 298 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: the structures are based on a total of 1811 restraints: 1709 NOE-derived distance constraints, 60 dihedral angle restraints, 42 distance restraints from hydrogen bonds. | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 8 |