[English] 日本語
![](img/lk-miru.gif)
- PDB-5mzz: Crystal structure of the decarboxylase AibA/AibB in complex with ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5mzz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the decarboxylase AibA/AibB in complex with 3-methylglutaconate | ||||||
![]() | (Glutaconate CoA-transferase family, subunit ...) x 2 | ||||||
![]() | LYASE / decarboxylase / CoA transferase like fold / 3-methylglutaconate | ||||||
Function / homology | CoA-transferase activity / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / 3-methylpent-2-enedioic acid / ACETATE ION / Glutaconate CoA-transferase family, subunit B / Glutaconate CoA-transferase family, subunit A![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bock, T. / Luxenburger, E. / Hoffmann, J. / Schuetza, V. / Feiler, C. / Mueller, R. / Blankenfeldt, W. | ||||||
![]() | ![]() Title: AibA/AibB Induces an Intramolecular Decarboxylation in Isovalerate Biosynthesis by Myxococcus xanthus. Authors: Bock, T. / Luxenburger, E. / Hoffmann, J. / Schutza, V. / Feiler, C. / Muller, R. / Blankenfeldt, W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 359.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 294 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 483.1 KB | Display | |
Data in XML | ![]() | 38.4 KB | Display | |
Data in CIF | ![]() | 54.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mzwSC ![]() 5mzxC ![]() 5mzyC ![]() 5n00C ![]() 5n01C ![]() 5n02C ![]() 5n03C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Glutaconate CoA-transferase family, subunit ... , 2 types, 4 molecules ACDB
#1: Protein | Mass: 28367.838 Da / Num. of mol.: 2 / Mutation: K191A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DK 1622 / Gene: MXAN_4264 / Production host: ![]() ![]() #2: Protein | Mass: 26280.871 Da / Num. of mol.: 2 / Mutation: E200A, E201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DK 1622 / Gene: MXAN_4265 / Production host: ![]() ![]() |
---|
-Non-polymers , 4 types, 375 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/8EW.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/8EW.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.98 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.085 M sodium acetate, 0.17 M ammonium acetate, 15 % glycerol, 25 % PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() | ||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 21, 2014 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.3→26.82 Å / Num. obs: 47619 / % possible obs: 99.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 16.59 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.099 / Rrim(I) all: 0.204 / Net I/σ(I): 6.6 / Num. measured all: 200861 / Scaling rejects: 0 | ||||||||||||||||||
Reflection shell |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5MZW Resolution: 2.3→26.82 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.91
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.74 Å2 / Biso mean: 20.3883 Å2 / Biso min: 9.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→26.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
|