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Yorodumi- PDB-2ju1: Solution structure of acyl carrier protein domain from module 2 o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ju1 | ||||||
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Title | Solution structure of acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS) | ||||||
Components | Erythronolide synthase | ||||||
Keywords | TRANSFERASE / carrier protein domain / modular polyketide synthase / alpha-helical bundle / Acyltransferase / Antibiotic biosynthesis / Multifunctional enzyme / NADP / Phosphopantetheine | ||||||
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 Similarity search - Function | ||||||
Biological species | Saccharopolyspora erythraea (bacteria) | ||||||
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) | ||||||
Authors | Alekseyev, V.Y. / Liu, C.W. / Puglisi, J.D. / Khosla, C. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ju1.cif.gz | 834.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ju1.ent.gz | 723.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ju1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/2ju1 ftp://data.pdbj.org/pub/pdb/validation_reports/ju/2ju1 | 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: 10160.617 Da / Num. of mol.: 1 / Fragment: acyl carrier protein domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) Description: stop codon at the C-terminus, before the C-terminal His-tag present in the plasmid Gene: eryA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.8 mM / Component: acyl carrier protein / Isotopic labeling: [U-13C; U-15N] |
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 with 4000 steps per structure. | ||||||||||||
NMR constraints | NOE constraints total: 1791 / NOE intraresidue total count: 327 / NOE long range total count: 438 / NOE medium range total count: 540 / NOE sequential total count: 486 / Protein phi angle constraints total count: 50 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 30 / Maximum upper distance constraint violation: 0.4 Å |