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- PDB-2ju2: Minimized mean solution structure of the acyl carrier protein dom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ju2 | ||||||
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Title | Minimized mean solution structure of the acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS) | ||||||
![]() | Erythronolide synthase | ||||||
![]() | TRANSFERASE / carrier protein domain / modular polyketide synthase / alpha-helical bundle / Acyltransferase / Antibiotic biosynthesis / Multifunctional enzyme / NADP / Phosphopantetheine | ||||||
Function / homology | ![]() 6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Model details | residues 5-95 are identical to the DEBS residues 3318-3408 (EryA, EntrezProtein accession no. AAA26493) | ||||||
Model type details | minimized average | ||||||
![]() | Alekseyev, V.Y. / Liu, C.W. / Puglisi, J.D. / Khosla, C. | ||||||
![]() | ![]() Title: Solution structure and proposed domain domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase. Authors: Alekseyev, V.Y. / Liu, C.W. / Cane, D.E. / Puglisi, J.D. / Khosla, C. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.2 KB | Display | ![]() |
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PDB format | ![]() | 27.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 242.6 KB | Display | ![]() |
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Full document | ![]() | 242.4 KB | Display | |
Data in XML | ![]() | 3.7 KB | Display | |
Data in CIF | ![]() | 4.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 10160.617 Da / Num. of mol.: 1 / Fragment: acyl carrier protein domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: stop codon at the C-terminus, before the C-terminal His-tag present in the expression vector plasmid Gene: eryA / Plasmid: pET28(a) / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: Q03131, 6-deoxyerythronolide-B synthase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: residues 5-95 are identical to the DEBS residues 3318-3408 (EryA, EntrezProtein accession no. AAA26493) | ||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 0.8-1 mM [U-13C; U-15N] acyl carrier protein, 0.05 % sodium azide, 30 mM sodium phosphate, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 30 / pH: 5.5 / Pressure: ambient / Temperature: 288 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: The standard simulated annealing protocol included as part of DYANA software was used to calculate a total of 50 structures, of which 30 structures with the lowest target function values ...Details: The standard simulated annealing protocol included as part of DYANA software was used to calculate a total of 50 structures, of which 30 structures with the lowest target function values were chosen for the solution structure ensemble. The helical regions of these 30 structures were superimposed and the mean structure was obtained using MOLMOL software, then subjected to the standard variable target function minimization implemented in DYANA. The resulting minimized mean structure is deposited here. The ensemble of 30 structures is deposited in the PDB entry 2ju1. | ||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 1 |