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Yorodumi- PDB-7agp: Structure of the AcylTransferase domain of Mycocerosic Acid Synth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7agp | ||||||
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Title | Structure of the AcylTransferase domain of Mycocerosic Acid Synthase from Mycobacterium tuberculosis | ||||||
Components | Mycocerosic acid synthase | ||||||
Keywords | TRANSFERASE / Mycocerosic Acid Synthase / AcylTransferase domain / polyketide synthase / Mycobacterium tuberculosis | ||||||
Function / homology | Function and homology information mycocerosate synthase / mycocerosate synthase activity / phosphopantetheine binding / ligase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / hydrolase activity / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium bovis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Brison, Y. / Nahoum, V. / Mourey, L. / Maveyraud, L. | ||||||
Funding support | France, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Molecular Basis for Extender Unit Specificity of Mycobacterial Polyketide Synthases. Authors: Grabowska, A.D. / Brison, Y. / Maveyraud, L. / Gavalda, S. / Faille, A. / Nahoum, V. / Bon, C. / Guilhot, C. / Pedelacq, J.D. / Chalut, C. / Mourey, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7agp.cif.gz | 330.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7agp.ent.gz | 271.6 KB | Display | PDB format |
PDBx/mmJSON format | 7agp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/7agp ftp://data.pdbj.org/pub/pdb/validation_reports/ag/7agp | HTTPS FTP |
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-Related structure data
Related structure data | 7agqC 7agrC 7agsC 7agtC 7aguC 7ahbC 7akcC 3tzwS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46470.418 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: mas, BQ2027_MB2965C / Production host: Escherichia coli (E. coli) / References: UniProt: Q02251, mycocerosate synthase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.53 Å3/Da / Density % sol: 65.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 1.1 M sodium succinate 0.1 M sodium acetate buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.3 Å / Num. obs: 51153 / % possible obs: 99.1 % / Redundancy: 3.54 % / Biso Wilson estimate: 74.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.05 / Rsym value: 0.042 / Net I/σ(I): 15.77 |
Reflection shell | Resolution: 2.4→2.54 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 8121 / CC1/2: 0.658 / Rrim(I) all: 0.998 / Rsym value: 0.845 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TZW Resolution: 2.4→49.3 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.243 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.243 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.189
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Displacement parameters | Biso mean: 85.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→49.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.42 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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