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Yorodumi- PDB-1pzr: Structure of fused docking domains from the erythromycin polyketi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pzr | ||||||
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Title | Structure of fused docking domains from the erythromycin polyketide synthase (DEBS), a model for the interaction between DEBS2 and DEBS3: the B 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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Remark 999 | SEQUENCE LEU 81 and MET 82 form a linker between the C-terminal fragment of DEBS2 and the N- ...SEQUENCE LEU 81 and MET 82 form a linker between the C-terminal fragment of DEBS2 and the N-terminal fragment of DEBS3 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pzr.cif.gz | 260.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pzr.ent.gz | 215.2 KB | Display | PDB format |
PDBx/mmJSON format | 1pzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/1pzr ftp://data.pdbj.org/pub/pdb/validation_reports/pz/1pzr | 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: 6842.579 Da / Num. of mol.: 2 / Fragment: RESIDUES 61-120 Source method: isolated from a genetically manipulated source Details: C-terminal fragment of DEBS2 fused to N-terminal fragment of DEBS3 Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: ERYA / Plasmid: pGEX4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS References: UniProt: Q03132, UniProt: Q03133, 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 1754 restraints: 1618 NOE-derived distance restraints, 78 dihedral angle restraints, 58 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: 100 / Conformers submitted total number: 7 |