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Yorodumi- PDB-5mzz: Crystal structure of the decarboxylase AibA/AibB in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mzz | ||||||
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Title | Crystal structure of the decarboxylase AibA/AibB in complex with 3-methylglutaconate | ||||||
Components | (Glutaconate CoA-transferase family, subunit ...) x 2 | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Myxococcus xanthus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Bock, T. / Luxenburger, E. / Hoffmann, J. / Schuetza, V. / Feiler, C. / Mueller, R. / Blankenfeldt, W. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mzz.cif.gz | 359.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mzz.ent.gz | 294 KB | Display | PDB format |
PDBx/mmJSON format | 5mzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/5mzz ftp://data.pdbj.org/pub/pdb/validation_reports/mz/5mzz | HTTPS FTP |
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-Related structure data
Related structure data | 5mzwSC 5mzxC 5mzyC 5n00C 5n01C 5n02C 5n03C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Myxococcus xanthus (strain DK 1622) (bacteria) Strain: DK 1622 / Gene: MXAN_4264 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D4I4 #2: Protein | Mass: 26280.871 Da / Num. of mol.: 2 / Mutation: E200A, E201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria) Strain: DK 1622 / Gene: MXAN_4265 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D4I3 |
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-Non-polymers , 4 types, 375 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.98 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å | ||||||||||||||||||
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 |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS 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
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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
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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: 17
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