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Yorodumi- PDB-7b4s: Structure of the 4'-phosphopantetheinyl transferase PptAb from My... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b4s | ||||||||||||
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Title | Structure of the 4'-phosphopantetheinyl transferase PptAb from Mycobacterium abscessus in complex with Coenzyme A and compound 153786 from the NCI Open Database | ||||||||||||
Components | Possible 4'-phosphopantetheinyl transferase | ||||||||||||
Keywords | TRANSFERASE / mycobacterium abscessus 4'-phosphopantetheinyl transferase complex | ||||||||||||
Function / homology | Function and homology information enterobactin synthetase complex / enterobactin biosynthetic process / holo-[acyl-carrier-protein] synthase activity / magnesium ion binding Similarity search - Function | ||||||||||||
Biological species | Mycobacteroides abscessus ATCC 19977 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.38 Å | ||||||||||||
Authors | Maveyraud, L. / Carivenc, C. / Mourey, L. | ||||||||||||
Funding support | France, 3items
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Citation | Journal: Sci Rep / Year: 2021 Title: Phosphopantetheinyl transferase binding and inhibition by amidino-urea and hydroxypyrimidinethione compounds. Authors: Carivenc, C. / Maveyraud, L. / Blanger, C. / Ballereau, S. / Roy-Camille, C. / Nguyen, M.C. / Genisson, Y. / Guilhot, C. / Chalut, C. / Pedelacq, J.D. / Mourey, L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b4s.cif.gz | 168.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b4s.ent.gz | 121.8 KB | Display | PDB format |
PDBx/mmJSON format | 7b4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b4s_validation.pdf.gz | 758.3 KB | Display | wwPDB validaton report |
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Full document | 7b4s_full_validation.pdf.gz | 758.4 KB | Display | |
Data in XML | 7b4s_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 7b4s_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/7b4s ftp://data.pdbj.org/pub/pdb/validation_reports/b4/7b4s | HTTPS FTP |
-Related structure data
Related structure data | 7b4rC 7bczC 7bdwC 6qygS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 25432.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacteroides abscessus ATCC 19977 (bacteria) Gene: MAB_3117c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1MD73 | ||||
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#2: Chemical | ChemComp-P62 / | ||||
#3: Chemical | ChemComp-COA / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.39 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M LiSO4 0.1 M MES pH 6.5 20 % (w/v) PEG8K 1 nmol NCI-P62 (dry compound) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.38→46.53 Å / Num. obs: 115854 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 22.29 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.068 / Rsym value: 0.065 / Net I/σ(I): 8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6QYG Resolution: 1.38→46.53 Å / SU ML: 0.2531 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 28.4779 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 31.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→46.53 Å
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Refine LS restraints |
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LS refinement shell |
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