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Yorodumi- PDB-1n3b: Crystal Structure of Dephosphocoenzyme A kinase from Escherichia coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n3b | ||||||
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Title | Crystal Structure of Dephosphocoenzyme A kinase from Escherichia coli | ||||||
Components | Dephospho-CoA kinase | ||||||
Keywords | TRANSFERASE / trimer / P-loop / alpha/beta / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics | ||||||
Function / homology | Function and homology information dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | O'Toole, N. / Barbosa, J.A.R.G. / Li, Y. / Hung, L.-W. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: Crystal Structure of a Trimeric Form of Dephosphocoenzyme A Kinase from Escherichia coli Authors: O'Toole, N. / Barbosa, J.A.R.G. / Li, Y. / Hung, L.-W. / Matte, A. / Cygler, M. #1: Journal: J.Struct.Biol. / Year: 2001 Title: Crystal Structure of Dephospho-coenzyme A Kinase from Haemophilus influenzae Authors: Oblomova, G. / Teplyakov, A. / Bonander, N. / Eisenstein, E. / Howard, A. / Gilliland, G. #2: Journal: J.Bacteriol. / Year: 2001 Title: Identification of yace (coaE) as the Structural Gene for Dephosphocoenzyme A Kinase in Escherichia coli K-12 Authors: Mishra, P.K. / Park, P.K. / Drueckhammer, D.G. #3: Journal: J.Mol.Biol. / Year: 1998 Title: The structure of a Trimeric Archael Adenylate Kinase Authors: Vorhein, C. / Bonisch, H. / Schafer, G. / Schulz, G.E. #4: Journal: Biochem.J. / Year: 1983 Title: A Bifunctional Enzyme Complex in Coenzyme A Biosynthesis: Purification of Pantetheine Phosphate Adenylyltransferase and Dephospho-CoA Kinase Authors: Worral, D.M. / Tubbs, P.K. #5: Journal: Biochem.J. / Year: 2002 Title: Identification and Characterization of the Gene Encoding the Human Adenylyltransferase and Dephosphocoenzyme A Kinase Bifunctional Enzyme Authors: Aghajanian, S. / Worral, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n3b.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n3b.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 1n3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n3b_validation.pdf.gz | 463 KB | Display | wwPDB validaton report |
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Full document | 1n3b_full_validation.pdf.gz | 476.7 KB | Display | |
Data in XML | 1n3b_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 1n3b_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/1n3b ftp://data.pdbj.org/pub/pdb/validation_reports/n3/1n3b | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24037.652 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: COAE / Plasmid: pET20b derivative / Production host: Escherichia coli (E. coli) / Strain (production host): DL41(DE3) / References: UniProt: P0A6I9, dephospho-CoA kinase #2: Chemical | ChemComp-SO4 / #3: 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: 2.45 Å3/Da / Density % sol: 49.44 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, cacodylate buffer, ammonium sulfate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97957, 0.97941 | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2001 / Details: monochromating crystal | |||||||||
Radiation | Monochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→40 Å / Num. obs: 59512 / % possible obs: 86.3 % / Redundancy: 6.7 % / Rsym value: 0.065 / Net I/σ(I): 26.1 | |||||||||
Reflection shell | Resolution: 1.81→1.88 Å / Num. unique all: 5096 / Rsym value: 0.439 / % possible all: 74.3 | |||||||||
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 56459 / % possible obs: 88.7 % / Num. measured all: 380533 / Rmerge(I) obs: 0.063 | |||||||||
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.87 Å / % possible obs: 71.1 % / Rmerge(I) obs: 0.546 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→40 Å / Isotropic thermal model: isotropic / Cross valid method: Free-R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Bulk solvent correction employed. The structure was refined using Friedel's pairs.
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Displacement parameters | Biso mean: 28.46 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→40 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 40 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.008 |