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Yorodumi- PDB-5yrr: The crystal structure of Phosphopantetheine adenylyltransferase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yrr | ||||||
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Title | The crystal structure of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Coenzyme A at 2.88 A resolution | ||||||
Components | Phosphopantetheine adenylyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
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 | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å | ||||||
Authors | Bairagya, H.R. / Gupta, A. / Iqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To Be Published Title: The crystal structure of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Coenzyme A at 2.88 A resolution Authors: Bairagya, H.R. / Gupta, A. / Iqbal, N. / Kaur, 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 | 5yrr.cif.gz | 50.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yrr.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 5yrr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/5yrr ftp://data.pdbj.org/pub/pdb/validation_reports/yr/5yrr | HTTPS FTP |
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-Related structure data
Related structure data | 5yh7S 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
#1: Protein | Mass: 18479.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: coaD / Production host: Escherichia coli (E. coli) References: UniProt: A0A059ZFC5, UniProt: B0VTH7*PLUS, pantetheine-phosphate adenylyltransferase | ||
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#2: Chemical | ChemComp-COA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.7 Å3/Da / Density % sol: 78.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1M LITHIUM SULPHATE, 0.5M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2017 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→65.2 Å / Num. obs: 10184 / % possible obs: 99.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.88→2.933 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.7 / Num. unique obs: 501 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YH7 Resolution: 2.88→65.2 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.883 / SU B: 15.539 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.312 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.541 Å2
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Refinement step | Cycle: 1 / Resolution: 2.88→65.2 Å
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Refine LS restraints |
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