[English] 日本語
![](img/lk-miru.gif)
- PDB-7ule: F420-1/GDP complex of F420-gamma glutamyl ligase (CofE) from Arch... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ule | ||||||
---|---|---|---|---|---|---|---|
Title | F420-1/GDP complex of F420-gamma glutamyl ligase (CofE) from Archaeoglobus fulgidus | ||||||
![]() | Coenzyme F420:L-glutamate ligase | ||||||
![]() | LIGASE / ligase substrate complex | ||||||
Function / homology | ![]() coenzyme F420-0:L-glutamate ligase / coenzyme F420-1:gamma-L-glutamate ligase / coenzyme F420-0:L-glutamate ligase activity / coenzyme F420-1:gamma-L-glutamate ligase activity / F420-0 metabolic process / GTP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bashiri, G. / Squire, C.J. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: A Universal Mechanism for Poly-glutamylation Authors: Bashiri, G. / Bramley, W. / Bulloch, E. / Stutely, S. / Middleditch, M. / Young, P. / Naqvi, M. / Harris, P. / Baker, E.N. / Squire, C.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 72.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 48.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uldC ![]() 7ulfC ![]() 2phnS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27423.568 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cofE, AF_2256 / Production host: ![]() ![]() References: UniProt: O28028, coenzyme F420-0:L-glutamate ligase, coenzyme F420-1:gamma-L-glutamate ligase |
---|
-Non-polymers , 5 types, 141 molecules ![](data/chem/img/GDP.gif)
![](data/chem/img/F4I.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F4I.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GDP / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-F4I / ( | ||||
#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.77 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.8 M ammonium sulfate, 0.1 M citrate pH 4.5, 2 mM GTP, 5 mM Mn2+, 1 mM F420-1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.9 Å / Num. obs: 25326 / % possible obs: 100 % / Redundancy: 26.7 % / CC1/2: 0.998 / Rpim(I) all: 0.019 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 27.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1320 / CC1/2: 0.538 / Rpim(I) all: 0.653 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2PHN Resolution: 1.7→48.896 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.218 / SU B: 3.129 / SU ML: 0.099 / Average fsc free: 0.8901 / Average fsc work: 0.9038 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.119 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.915 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→48.896 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|