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Yorodumi- PDB-8i8i: Crystal structure of Phosphopantetheine adenylyltransferase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i8i | |||||||||
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Title | Crystal structure of Phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59 A resolution | |||||||||
Components | Phosphopantetheine adenylyltransferase | |||||||||
Keywords | TRANSFERASE / coaD / PPAT / COENZYME A biosynthesis | |||||||||
Function / homology | Function and homology information pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | |||||||||
Authors | Ahmad, N. / Singh, P.K. / Sharma, P. / Sharma, S. / Singh, T.P. | |||||||||
Funding support | India, 1items
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Citation | Journal: Eur.Biophys.J. / Year: 2024 Title: Structure of a novel form of phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59 angstrom resolution. Authors: Ahmad, N. / Sharma, P. / Sharma, S. / Singh, T.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i8i.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i8i.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 8i8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/8i8i ftp://data.pdbj.org/pub/pdb/validation_reports/i8/8i8i | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17684.543 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: coaD, kdtB / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9XC89, pantetheine-phosphate adenylyltransferase #2: Chemical | ChemComp-EDO / | #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: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 20% PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→41.27 Å / Num. obs: 17572 / % possible obs: 99.7 % / Redundancy: 4 % / Biso Wilson estimate: 48.8 Å2 / CC1/2: 0.998 / Net I/σ(I): 3.21 |
Reflection shell | Resolution: 2.59→2.67 Å / Num. unique obs: 632 / CC1/2: 0.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→41.27 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.709 / SU ML: 0.287 / Cross valid method: FREE R-VALUE / ESU R: 0.893 / ESU R Free: 0.32 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.056 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→41.27 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: 20
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