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Yorodumi- PDB-3x1j: Crystal Structure of Phosphopantetheine adenylyltransferase (PPAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3x1j | ||||||
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Title | Crystal Structure of Phosphopantetheine adenylyltransferase (PPAT/CoaD) with AcCoA from Pseudomonas aeruginosa | ||||||
Components | Phosphopantetheine adenylyltransferase | ||||||
Keywords | TRANSFERASE / Rossmann Fold | ||||||
Function / homology | Function and homology information [citrate (pro-3S)-lyase] ligase activity / pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa 2192 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.334 Å | ||||||
Authors | Chatterjee, R. / Datta, S. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2016 Title: Transition of phosphopantetheine adenylyltransferase from catalytic to allosteric state is characterized by ternary complex formation in Pseudomonas aeruginosa Authors: Chatterjee, R. / Mondal, A. / Basu, A. / Datta, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x1j.cif.gz | 109.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x1j.ent.gz | 86.4 KB | Display | PDB format |
PDBx/mmJSON format | 3x1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3x1j_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3x1j_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3x1j_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 3x1j_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/3x1j ftp://data.pdbj.org/pub/pdb/validation_reports/x1/3x1j | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 17795.473 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa 2192 (bacteria) / Strain: 2192 / Gene: coaD, PA0363, PA2G_04277 / Production host: Escherichia coli (E. coli) References: UniProt: A3LHH1, UniProt: A0A0X1KGP2*PLUS, pantetheine-phosphate adenylyltransferase |
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-Non-polymers , 6 types, 53 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-DMS / #6: Chemical | ChemComp-PEG / | #7: 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: 2.67 Å3/Da / Density % sol: 53.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: PEG4000 18%, 0.1M HEPES, 5% Isopropanol, 200mM Sodium acetate., pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9748 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9748 Å / Relative weight: 1 |
Reflection | Resolution: 2.334→45.328 Å / Num. obs: 24934 / % possible obs: 99.9 % / Observed criterion σ(I): 1.8 |
Reflection shell | Resolution: 2.33→2.47 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.334→45.328 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 27.32 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.334→45.328 Å
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Refine LS restraints |
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LS refinement shell |
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