[English] 日本語
![](img/lk-miru.gif)
- PDB-6dyn: C-terminal condensation domain of Ebony in complex with Histamine -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6dyn | ||||||
---|---|---|---|---|---|---|---|
Title | C-terminal condensation domain of Ebony in complex with Histamine | ||||||
![]() | Ebony | ||||||
![]() | BIOSYNTHETIC PROTEIN / NRPS / Condensation domain / Peptide-bond formation | ||||||
Function / homology | ![]() ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Izore, T. / Tailhades, J. / Hansen, M.H. / Kaczmarski, J.A. / Jackson, C.J. / Cryle, M.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Drosophila melanogasternonribosomal peptide synthetase Ebony encodes an atypical condensation domain. Authors: Izore, T. / Tailhades, J. / Hansen, M.H. / Kaczmarski, J.A. / Jackson, C.J. / Cryle, M.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 63.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 43.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 435.4 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dymSC ![]() 6dyoC ![]() 6dyrC ![]() 6dysC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 25991.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-HSM / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.24 % / Description: Long thin needles |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, PEG 400, CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40.97 Å / Num. obs: 13655 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 27.6 Å2 / Rpim(I) all: 0.05 / Net I/av σ(I): 11.9 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.1→2.16 Å / Mean I/σ(I) obs: 2 / CC1/2: 0.63 / Rpim(I) all: 0.4 |
-
Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6DYM Resolution: 2.102→40.97 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.102→40.97 Å
|