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Yorodumi- PDB-6rcx: Mycobacterial 4'-phosphopantetheinyl transferase PptAb in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rcx | |||||||||
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Title | Mycobacterial 4'-phosphopantetheinyl transferase PptAb in complex with the ACP domain of PpsC. | |||||||||
Components |
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Keywords | TRANSFERASE/TRANSPORT PROTEIN / TRANSFERASE-TRANSPORT PROTEIN complex | |||||||||
Function / homology | Function and homology information (phenol)carboxyphthiodiolenone synthase / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / Actinobacterium-type cell wall biogenesis / enterobactin synthetase complex / enterobactin biosynthetic process / holo-[acyl-carrier-protein] synthase activity / DIM/DIP cell wall layer assembly / fatty acid synthase activity ...(phenol)carboxyphthiodiolenone synthase / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / Actinobacterium-type cell wall biogenesis / enterobactin synthetase complex / enterobactin biosynthetic process / holo-[acyl-carrier-protein] synthase activity / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / magnesium ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacteroides abscessus ATCC 19977 (bacteria) Mycobacterium abscessus ATCC 19977 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Nguyen, M.C. / Mourey, L. / Pedelacq, J.D. | |||||||||
Funding support | France, 2items
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Citation | Journal: Febs J. / Year: 2020 Title: Conformational flexibility of coenzyme A and its impact on the post-translational modification of acyl carrier proteins by 4'-phosphopantetheinyl transferases. Authors: Nguyen, M.C. / Saurel, O. / Carivenc, C. / Gavalda, S. / Saitta, S. / Tran, M.P. / Milon, A. / Chalut, C. / Guilhot, C. / Mourey, L. / Pedelacq, J.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rcx.cif.gz | 138.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rcx.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 6rcx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/6rcx ftp://data.pdbj.org/pub/pdb/validation_reports/rc/6rcx | HTTPS FTP |
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-Related structure data
Related structure data | 6qwuC 6qxqC 6qxrC 6qyfC 6qygC 4u89S 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#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: Protein | Mass: 16791.650 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ACP fragment from position 2056 to 2188 mutation S2105A Source: (gene. exp.) Mycobacterium abscessus ATCC 19977 (bacteria) Strain: ATCC 25618 / H37Rv / Gene: ppsC, Rv2933 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P96202, beta-ketoacyl-[acyl-carrier-protein] synthase I |
-Non-polymers , 4 types, 149 molecules
#3: Chemical | ChemComp-COA / | ||||
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#4: Chemical | #5: Chemical | ChemComp-CAC / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Na Cacodylate 30 % PEG 8K 0.2 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 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: 2→41.15 Å / Num. obs: 23870 / % possible obs: 99.6 % / Redundancy: 5.4 % / CC1/2: 0.998 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2→2.072 Å / Num. unique obs: 12069 / CC1/2: 0.929 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4u89 Resolution: 2→41.15 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.45 Å2 / Biso mean: 50.3859 Å2 / Biso min: 22.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→41.15 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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