[English] 日本語
![](img/lk-miru.gif)
- PDB-5sxy: The solution NMR structure for the PqqD truncation of Methylobact... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5sxy | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The solution NMR structure for the PqqD truncation of Methylobacterium extorquens PqqCD representing a functional and stand-alone ribosomally synthesized and post-translational modified (RiPP) recognition element (RRE) | |||||||||
![]() | Bifunctional coenzyme PQQ synthesis protein C/D | |||||||||
![]() | CHAPERONE / RiPP RRE peptide scaffolding | |||||||||
Function / homology | ![]() pyrroloquinoline-quinone synthase / pyrroloquinoline-quinone synthase activity / pyrroloquinoline quinone biosynthetic process / : / sulfur compound metabolic process / quinone binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
![]() | Evans, R.L. / Xia, Y. / Wilmot, C.M. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Nuclear Magnetic Resonance Structure and Binding Studies of PqqD, a Chaperone Required in the Biosynthesis of the Bacterial Dehydrogenase Cofactor Pyrroloquinoline Quinone. Authors: Evans, R.L. / Latham, J.A. / Xia, Y. / Klinman, J.P. / Wilmot, C.M. #1: ![]() Title: 1H, 13C, and 15N resonance assignments and secondary structure information for Methylobacterium extorquens PqqD and the complex of PqqD with PqqA Authors: Evans, R.L. / Latham, J.A. / Klinman, J.P. / Wilmot, C.M. / Xia, Y. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 571.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 479.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 401.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 515.7 KB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 48.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-
Components
#1: Protein | Mass: 10421.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 14718 / DSM 1338 / AM1 / Gene: pqqCD, MexAM1_META1p1749 / Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: Q49150, pyrroloquinoline-quinone synthase |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-
Sample preparation
Details | Type: solution / Contents: 4.6 mg/mL [U-13C; U-15N] PqqD, 95% H2O/5% D2O Details: PqqD sample contained 285 micro-L of 5.0 mg/ml (0.40 mM) 13C-, 15N-labeled M.ex.PqqD in 25 mM potassium phosphate, pH 6.5, 7 micro-L of 50 mM sodium azide, and 15 micro-L HPLC grade D2O. ...Details: PqqD sample contained 285 micro-L of 5.0 mg/ml (0.40 mM) 13C-, 15N-labeled M.ex.PqqD in 25 mM potassium phosphate, pH 6.5, 7 micro-L of 50 mM sodium azide, and 15 micro-L HPLC grade D2O. Final concentrations: 4.6 mg/ml (0.37 mM) MexPqqD, 1.1 mM sodium azide, 4.9% D2O). Label: PqqD / Solvent system: 95% H2O/5% D2O |
---|---|
Sample | Conc.: 4.6 mg/mL / Component: PqqD / Isotopic labeling: [U-13C; U-15N] |
Sample conditions | Details: PqqD sample contained 285 micro-L of 5.0 mg/ml (0.40 mM) 13C-, 15N-labeled M.ex.PqqD in 25 mM potassium phosphate, pH 6.5, 7 micro-L of 50 mM sodium azide, and 15 micro-L HPLC grade D2O. ...Details: PqqD sample contained 285 micro-L of 5.0 mg/ml (0.40 mM) 13C-, 15N-labeled M.ex.PqqD in 25 mM potassium phosphate, pH 6.5, 7 micro-L of 50 mM sodium azide, and 15 micro-L HPLC grade D2O. Final concentrations: 4.6 mg/ml (0.37 mM) MexPqqD, 1.1 mM sodium azide, 4.9% D2O). Ionic strength: 25 mM / Label: PqqD / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
|
---|
-
Processing
NMR software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 6 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |