[English] 日本語
![](img/lk-miru.gif)
- PDB-8gju: Crystal structure of human methylmalonyl-CoA mutase (MMUT) in com... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8gju | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human methylmalonyl-CoA mutase (MMUT) in complex with methylmalonic acidemia type A protein (MMAA), coenzyme A, and GDP | |||||||||
![]() |
| |||||||||
![]() | Isomerase/Hydrolase / protein-protein complex / isomerase / GTPase / G-protein / cobalamin / vitamin B12 / transport / organometallic cofactor / Isomerase-Hydrolase complex | |||||||||
Function / homology | ![]() Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / Propionyl-CoA catabolism / methylmalonyl-CoA mutase / cobalamin metabolic process / Cobalamin (Cbl) metabolism / methylmalonyl-CoA mutase activity / Hydrolases; Acting on acid anhydrides / sulfur compound metabolic process / cobalamin binding ...Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / Propionyl-CoA catabolism / methylmalonyl-CoA mutase / cobalamin metabolic process / Cobalamin (Cbl) metabolism / methylmalonyl-CoA mutase activity / Hydrolases; Acting on acid anhydrides / sulfur compound metabolic process / cobalamin binding / mitochondrial matrix / GTPase activity / GTP binding / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mascarenhas, R.M. / Ruetz, M. / Gouda, H. / Yaw, M. / Banerjee, R. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B 12 delivery and repair. Authors: Mascarenhas, R. / Ruetz, M. / Gouda, H. / Heitman, N. / Yaw, M. / Banerjee, R. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 771.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 619.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 141.8 KB | Display | |
Data in CIF | ![]() | 186.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wwwS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 8 molecules DFABJKLH
#1: Protein | Mass: 38718.867 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8IVH4, Hydrolases; Acting on acid anhydrides #2: Protein | Mass: 83009.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 4 types, 25 molecules ![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GDP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-COA / #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.99 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Morpheus1-F11 (Molecular Dimensions): 120 mM monosaccharides mix, 100 mM buffer system 3, pH 8.5, 30% precipitant mix 3 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→117 Å / Num. obs: 74830 / % possible obs: 89 % / Redundancy: 3.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.092 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.794→3.074 Å / Rmerge(I) obs: 0.775 / Num. unique obs: 2737 / CC1/2: 0.562 / Rpim(I) all: 0.504 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2WWW Resolution: 2.79→80.62 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.92 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→80.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|