[English] 日本語
![](img/lk-miru.gif)
- PDB-2cbg: Crystal structure of the PMSF-inhibited thioesterase domain of th... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2cbg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the PMSF-inhibited thioesterase domain of the fengycin biosynthesis cluster | ||||||
![]() | FENGYCIN SYNTHETASE | ||||||
![]() | HYDROLASE / FENGYCIN THIOESTERASE / NON-RIBOSOMAL PEPTIDE SYNTHESIS / ALPHA/BETA-HYDROLASE / PHOSPHOPANTETHEINE | ||||||
Function / homology | ![]() amino acid activation for nonribosomal peptide biosynthetic process / carboxylic acid metabolic process / secondary metabolite biosynthetic process / phosphopantetheine binding / antibiotic biosynthetic process / catalytic activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Samel, S. / Marahiel, M.A. / Essen, L.-O. | ||||||
![]() | ![]() Title: The Thioesterase Domain of the Fengycin Biosynthesis Cluster: A Structural Base for the Macrocyclization of a Non-Ribosomal Lipopeptide Authors: Samel, S. / Wagner, B. / Marahiel, M.A. / Essen, L.-O. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 57.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 41 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 453.8 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cb9C ![]() 1jmkS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 27522.734 Da / Num. of mol.: 1 / Fragment: THIOESTERASE DOMAIN, RESIDUES 1043-1274 Source method: isolated from a genetically manipulated source Details: RECOMBINANT FRAGMENT OF THE NRPS SYNTHETASE FENB (Q1043-H1274), INHIBITED FORM GENERATED BY CRYSTALS SOAKED IN THE PRESENCE OF PMSF Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-PMS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % |
---|---|
Crystal grow | pH: 5.6 Details: 0.2 M NH4 ACETATE, 0.1 M NA CITRATE (PH 5.6), 22.5 % PEG 8000, 10 MG/ML PROTEIN |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2003 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→24 Å / Num. obs: 9190 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 3.76 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.5→2.56 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.4 / % possible all: 54.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JMK Resolution: 2.5→24 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.876 / SU B: 8.38 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.43 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE RESIDUES T123-A131 WERE DISORDERED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→24 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|