[English] 日本語
![](img/lk-miru.gif)
- PDB-7xbv: Crystal structure of the adenylation domain of CmnG in complex wi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7xbv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the adenylation domain of CmnG in complex with AMPCPP | ||||||
![]() | CmnG | ||||||
![]() | BIOSYNTHETIC PROTEIN / Adenylation | ||||||
Function / homology | ![]() amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / nucleotide binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, I.H. / Wang, Y.L. / Chang, C.Y. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Characterization and Structural Determination of CmnG-A, the Adenylation Domain That Activates the Nonproteinogenic Amino Acid Capreomycidine in Capreomycin Biosynthesis. Authors: Chen, I.H. / Cheng, T. / Wang, Y.L. / Huang, S.J. / Hsiao, Y.H. / Lai, Y.T. / Toh, S.I. / Chu, J. / Rudolf, J.D. / Chang, C.Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 100.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 72.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1002.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1005.3 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xbsC ![]() 7xbtC ![]() 7xbuSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 56242.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cmnG / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-APC / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.61 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.8 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 5.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→30 Å / Num. obs: 32099 / % possible obs: 99.3 % / Redundancy: 7.7 % / CC1/2: 0.975 / Net I/σ(I): 30.125 |
Reflection shell | Resolution: 1.94→2.02 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.93 / Num. unique obs: 3003 / CC1/2: 0.885 / % possible all: 94.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7XBU Resolution: 1.94→19.94 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.62 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.23 Å2 / Biso mean: 21.558 Å2 / Biso min: 6.83 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→19.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.945→1.995 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|