+Open data
-Basic information
Entry | Database: PDB / ID: 4mb2 | ||||||
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Title | Crystal structure of TON1374 in complex with ATP | ||||||
Components | Phosphopantothenate synthetase4-phosphopantoate—beta-alanine ligase | ||||||
Keywords | LIGASE / ATP binding | ||||||
Function / homology | Function and homology information 4-phosphopantoate-beta-alanine ligase / acid-amino acid ligase activity / coenzyme A biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Thermococcus onnurineus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å | ||||||
Authors | Kim, M.-K. / An, Y.J. / Cha, S.-S. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2013 Title: The crystal structure of a novel phosphopantothenate synthetase from the hyperthermophilic archaea, Thermococcus onnurineus NA1 Authors: Kim, M.-K. / An, Y.J. / Cha, S.-S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mb2.cif.gz | 211.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mb2.ent.gz | 171.6 KB | Display | PDB format |
PDBx/mmJSON format | 4mb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/4mb2 ftp://data.pdbj.org/pub/pdb/validation_reports/mb/4mb2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29732.498 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Gene: TON_1374 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YXQ1, EC: 6.3.2.26 #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / | #4: 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: 2.56 Å3/Da / Density % sol: 52.04 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 8.5 Details: 0.08M Tris-HCl, 24%(w/v) polyethylene glycol 4000, 4mM ATP, pH 8.5, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 26, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. all: 60918 / Num. obs: 60918 / % possible obs: 97.8 % / Observed criterion σ(I): 4.8 |
Reflection shell | Resolution: 2.19→2.23 Å / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.19→37.62 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.318 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.222 / 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 max: 171.19 Å2 / Biso mean: 48.6026 Å2 / Biso min: 11.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→37.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.192→2.249 Å / Total num. of bins used: 20
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