[English] 日本語
![](img/lk-miru.gif)
- PDB-7ruu: Structure of Human ATP:Cobalamin Adenosyltransferase R190C bound ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ruu | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Human ATP:Cobalamin Adenosyltransferase R190C bound to adenosylcobalamin | ||||||
![]() | Corrinoid adenosyltransferase | ||||||
![]() | TRANSFERASE / ATP:cobalamin adenosyl transferase / cobalamin / vitamin B12 / patient mutation | ||||||
Function / homology | ![]() Defective MMAB causes MMA, cblB type / cobalamin metabolic process / Cobalamin (Cbl) metabolism / corrinoid adenosyltransferase activity / transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / cobalamin binding / mitochondrial matrix / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mascarenhas, R. / Gouda, H. / Koutmos, M. / Banerjee, R. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Patient mutations in human ATP:cob(I)alamin adenosyltransferase differentially affect its catalytic versus chaperone functions. Authors: Gouda, H. / Mascarenhas, R. / Pillay, S. / Ruetz, M. / Koutmos, M. / Banerjee, R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 149.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 115.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7rutC ![]() 7ruvC ![]() 2idxS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 21666.643 Da / Num. of mol.: 4 / Mutation: R190C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 264 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/K.gif)
![](data/chem/img/5AD.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/5AD.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | ChemComp-5AD / #5: Chemical | ChemComp-B12 / #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 30% (v/v) 2-methyl-2,4-pentanediol, 100 mM sodium acetate pH 4.6, 20 mM calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→39.75 Å / Num. obs: 80886 / % possible obs: 99.8 % / Redundancy: 10.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.85→1.89 Å / Rmerge(I) obs: 0.11 / Num. unique obs: 4590 / CC1/2: 0.69 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2IDX Resolution: 1.85→36.159 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.39 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.2 Å2 / Biso mean: 42.0263 Å2 / Biso min: 20.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→36.159 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|