[English] 日本語
![](img/lk-miru.gif)
- PDB-2kgd: NMR Solution Structures of 3-oxo-butyl-ACP, an intermediate mimic... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2kgd | ||||||
---|---|---|---|---|---|---|---|
Title | NMR Solution Structures of 3-oxo-butyl-ACP, an intermediate mimic from the actinorhodin polyketide synthase in Streptomyces coelicolor | ||||||
![]() | Actinorhodin polyketide synthase acyl carrier protein | ||||||
![]() | BIOSYNTHETIC PROTEIN / ACP / polyketide mimic / diketide / Actinorhodin / Coelicolor / Antibiotic biosynthesis / Phosphopantetheine | ||||||
Function / homology | ![]() lipid A biosynthetic process / acyl binding / antibiotic biosynthetic process / acyl carrier activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Crump, M.P. / Evans, S.E. / Williams, C. | ||||||
![]() | ![]() Title: Probing the Interactions of Early Polyketide Intermediates with the Actinorhodin ACP from S. coelicolor A3(2). Authors: Evans, S.E. / Williams, C. / Arthur, C.J. / Ploskon, E. / Wattana-Amorn, P. / Cox, R.J. / Crosby, J. / Willis, C.L. / Simpson, T.J. / Crump, M.P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 566.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 500.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2kg6C ![]() 2kg8C ![]() 2kg9C ![]() 2kgaC ![]() 2kgcC ![]() 2kgeC C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-
Components
#1: Protein | Mass: 9239.177 Da / Num. of mol.: 1 / Mutation: C17S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-SXV / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-
Sample preparation
Details | Contents: 1-2 mM 4 -phosphopantetheine chain derivatised with a 3-oxo-butyl group-1, 20 mM potassium phosphate-2, 1 mM sodium azide-3, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||
Sample conditions | pH: 5.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
---|
-
Processing
NMR software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 Details: ALL STRUCTURE CALCULATIONS WERE CARRIED OUT USING THE AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT OF NOES (ARIA) PROTOCOL VERSION 1.2. THE 20 BEST STRUCTURES (SORTED ACCORDING TO TOTAL ...Details: ALL STRUCTURE CALCULATIONS WERE CARRIED OUT USING THE AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT OF NOES (ARIA) PROTOCOL VERSION 1.2. THE 20 BEST STRUCTURES (SORTED ACCORDING TO TOTAL ENERGY) WERE SELECTED FOR WATER REFINEMENT. WATER REFINED STRUCTURES WERE CALCULATED USING THE SLIGHTLY MODIFIED REFINEMENT SCRIPT APPLIED TO THE RECOORD DATABASE. PROCHECK AND WHATCHECK AND QUALITY INDICATORS WERE COMPARED TO THE AVERAGE VALUES FOR THE RECOORD DATABASE OF PROTEIN NMR STRUCTURES. | ||||||||||||||||||||||||
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: 20 |