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Yorodumi- PDB-2gtd: Crystal Structure of a Type III Pantothenate Kinase: Insight into... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gtd | ||||||
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Title | Crystal Structure of a Type III Pantothenate Kinase: Insight into the Catalysis of an Essential Coenzyme A Biosynthetic Enzyme Universally Distributed in Bacteria | ||||||
Components | Type III Pantothenate Kinase | ||||||
Keywords | TRANSFERASE / Type III Pantothenate Kinase | ||||||
Function / homology | Function and homology information pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Yang, K. / Eyobo, Y. / Brand, A.L. / Martynowski, D. / Tomchick, D. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2006 Title: Crystal Structure of a Type III Pantothenate Kinase: Insight into the Mechanism of an Essential Coenzyme A Biosynthetic Enzyme Universally Distributed in Bacteria. Authors: Yang, K. / Eyobo, Y. / Brand, L.A. / Martynowski, D. / Tomchick, D. / Strauss, E. / Zhang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gtd.cif.gz | 316.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gtd.ent.gz | 258.8 KB | Display | PDB format |
PDBx/mmJSON format | 2gtd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gtd_validation.pdf.gz | 465.4 KB | Display | wwPDB validaton report |
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Full document | 2gtd_full_validation.pdf.gz | 490.6 KB | Display | |
Data in XML | 2gtd_validation.xml.gz | 69.7 KB | Display | |
Data in CIF | 2gtd_validation.cif.gz | 99.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/2gtd ftp://data.pdbj.org/pub/pdb/validation_reports/gt/2gtd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The biological assembly is a hexamer generated from the dimer. |
-Components
#1: Protein | Mass: 27658.850 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pProEX-HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9WZY5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: 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: 2.23 Å3/Da / Density % sol: 44.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15% PEG-3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97872, 0.97886 | |||||||||
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Detector | Date: Dec 14, 2005 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2→31.56 Å / Num. obs: 95595 / % possible obs: 97.7 % / Observed criterion σ(F): 28.78 / Observed criterion σ(I): 5.59 | |||||||||
Reflection shell | Resolution: 2→2.05 Å / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→31.56 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.335 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.188 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 24.507 Å2
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Refinement step | Cycle: LAST / Resolution: 2→31.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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