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Yorodumi- PDB-6jnh: Crystal structure of the complex of Phosphopantetheine adenylyltr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jnh | ||||||
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Title | Crystal structure of the complex of Phosphopantetheine adenylyltransferasefrom Acinetobacter baumannii with Ascorbic acid (Vitamin-C) at 2.0A 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 Å | ||||||
Authors | Iqbal, N. / Gupta, A. / Sharm, P. / Singh, T.P. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Ascorbic acid (Vitamin-C) at 2.0A resolution Authors: Iqbal, N. / Gupta, A. / Sharm, P. / 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 | 6jnh.cif.gz | 50.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jnh.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 6jnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/6jnh ftp://data.pdbj.org/pub/pdb/validation_reports/jn/6jnh | HTTPS FTP |
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-Related structure data
Related structure data | 6j3mS 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A059ZFC5, pantetheine-phosphate adenylyltransferase | ||||||
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#2: Sugar | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: 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: 5.74 Å3/Da / Density % sol: 78.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1M LITHIUM SULPHATE, 0.5M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97119 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97119 Å / Relative weight: 1 |
Reflection | Resolution: 2→125.12 Å / Num. obs: 29100 / % possible obs: 97.7 % / Redundancy: 20 % / Rpim(I) all: 0.04 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 1461 / Rpim(I) all: 0.886 / % possible all: 68.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J3M Resolution: 2→125.12 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.426 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.657 Å2
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Refinement step | Cycle: 1 / Resolution: 2→125.12 Å
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