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Open data
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Basic information
Entry | Database: PDB / ID: 5n03 | ||||||
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Title | Crystal structure of the decarboxylase AibA/AibB C56V variant | ||||||
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![]() | LYASE / decarboxylase / CoA transferase like fold | ||||||
Function / homology | CoA-transferase activity / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / 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 | ![]() | 219 KB | Display | ![]() |
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PDB format | ![]() | 172 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.2 KB | Display | ![]() |
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Full document | ![]() | 450.3 KB | Display | |
Data in XML | ![]() | 45 KB | Display | |
Data in CIF | ![]() | 67.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mzwSC ![]() 5mzxC ![]() 5mzyC ![]() 5mzzC ![]() 5n00C ![]() 5n01C ![]() 5n02C 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
#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: 26276.859 Da / Num. of mol.: 2 / Mutation: C56V, E200A, E201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DK 1622 / Gene: MXAN_4265 / Production host: ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.05 % |
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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: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 3, 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: 2.05→19.54 Å / Num. obs: 67504 / % possible obs: 99.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 11.74 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.09 / Rrim(I) all: 0.187 / Net I/σ(I): 9.8 / Num. measured all: 284760 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MZW Resolution: 2.1→19.536 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.24 Å2 / Biso mean: 13.7851 Å2 / Biso min: 1.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→19.536 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: 23
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