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Yorodumi- PDB-8i8m: Crystal structure of the ternary complex of Phosphopantetheine ad... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i8m | ||||||
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Title | Crystal structure of the ternary complex of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with Coenzyme-A and Phosphonoacetic acid at 2.65 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 | Enterobacter sp. 638 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å | ||||||
Authors | Ahmad, N. / Sharma, P. / Sharma, S. / Singh, T.P. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the ternary complex of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with Coenzyme-A and Phosphonoacetic acid at 2.65 A 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 | 8i8m.cif.gz | 205.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i8m.ent.gz | 169.1 KB | Display | PDB format |
PDBx/mmJSON format | 8i8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/8i8m ftp://data.pdbj.org/pub/pdb/validation_reports/i8/8i8m | 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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3 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 18442.424 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter sp. 638 (bacteria) / Gene: coaD, Ent638_0105 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A4W515, pantetheine-phosphate adenylyltransferase |
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-Non-polymers , 5 types, 449 molecules
#2: Chemical | #3: Chemical | ChemComp-PAE / #4: Chemical | ChemComp-EDO / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-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: 2.7 Å3/Da / Density % sol: 54.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: BIS-TRIS propane pH 7.0, Sodium citrate tribasic dihydrate |
-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: 0.8731 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→42.68 Å / Num. obs: 31523 / % possible obs: 94.4 % / Redundancy: 2.1 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.984 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.65→2.72 Å / Num. unique obs: 1555 / CC1/2: 0.842 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.651→42.64 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.188 / Average fsc free: 0.9654 / Average fsc work: 0.9781 / Cross valid method: FREE R-VALUE / ESU R Free: 0.321 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: 44.413 Å2
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Refinement step | Cycle: LAST / Resolution: 2.651→42.64 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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