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Yorodumi- PDB-5kgs: Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kgs | ||||||
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Title | Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with an inhibitor optimized from HTS lead: 5-[4-(1,3-benzodioxol-5-ylcarbonyl)piperazin-1-yl]-2,3-dihydroinden-1-one | ||||||
Components | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | ||||||
Keywords | Transferase/Transferase inhibitor / transaminase / PLP / Transferase / Transferase-inhibitor complex / Transferase-Transferase inhibitor complex | ||||||
Function / homology | Function and homology information adenosylmethionine-8-amino-7-oxononanoate transaminase / dethiobiotin synthase activity / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium bovis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Maize, K.M. / Aldrich, C.C. / Finzel, B.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Med. Chem. / Year: 2017 Title: Structure-Based Optimization of Pyridoxal 5'-Phosphate-Dependent Transaminase Enzyme (BioA) Inhibitors that Target Biotin Biosynthesis in Mycobacterium tuberculosis. Authors: Liu, F. / Dawadi, S. / Maize, K.M. / Dai, R. / Park, S.W. / Schnappinger, D. / Finzel, B.C. / Aldrich, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kgs.cif.gz | 179.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kgs.ent.gz | 138.9 KB | Display | PDB format |
PDBx/mmJSON format | 5kgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/5kgs ftp://data.pdbj.org/pub/pdb/validation_reports/kg/5kgs | HTTPS FTP |
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-Related structure data
Related structure data | 4xjoC 4xjpC 5kgtC 4w1xS 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
#1: Protein | Mass: 48536.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) (bacteria) Strain: ATCC BAA-935 / AF2122/97 / Gene: bioA, Mb1595 / Production host: Escherichia coli (E. coli) References: UniProt: P0A4X7, adenosylmethionine-8-amino-7-oxononanoate transaminase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.19 Å3/Da / Density % sol: 43.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, 14% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.1→203.898 Å / Num. obs: 50729 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 23.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.041 / Rrim(I) all: 0.102 / Net I/σ(I): 14.4 / Num. measured all: 317821 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _ / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4W1X Resolution: 2.1→46.277 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.74 / 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: 79 Å2 / Biso mean: 22.4997 Å2 / Biso min: 8.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→46.277 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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