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- PDB-5mzx: Crystal structure of the decarboxylase AibA/AibB in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mzx | ||||||
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Title | Crystal structure of the decarboxylase AibA/AibB in complex with 4'-diphospho pantetheine | ||||||
![]() | (Glutaconate CoA-transferase family, subunit ...) x 2 | ||||||
![]() | LYASE / decarboxylase / CoA transferase like fold / coenzyme A | ||||||
Function / homology | CoA-transferase activity / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / 4'-diphospho pantetheine / 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 370.4 KB | Display | ![]() |
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PDB format | ![]() | 304.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 906.4 KB | Display | ![]() |
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Full document | ![]() | 932 KB | Display | |
Data in XML | ![]() | 39.9 KB | Display | |
Data in CIF | ![]() | 56.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mzwSC ![]() 5mzyC ![]() 5mzzC ![]() 5n00C ![]() 5n01C ![]() 5n02C ![]() 5n03C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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: ![]() ![]() |
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-Non-polymers , 4 types, 452 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/4PS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/4PS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.34 % |
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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 | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 14, 2014 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2→46.831 Å / Num. obs: 72195 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.59 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Net I/σ(I): 10.5 | ||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MZW Resolution: 2→46.831 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.74 Å2 / Biso mean: 30.7134 Å2 / Biso min: 14.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→46.831 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26 / % reflection obs: 100 %
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