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- PDB-4ttr: Crystal structure of Legionella pneumophila dephospho-CoA kinase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ttr | ||||||
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Title | Crystal structure of Legionella pneumophila dephospho-CoA kinase in complex with Bu2 | ||||||
![]() | Dephospho-CoA kinase | ||||||
![]() | TRANSFERASE / Kinase / P-loop / Coenzyme metabolism | ||||||
Function / homology | ![]() dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, D. / Ge, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Legionella pneumophila dephospho-CoA kinase reveals a non-canonical conformation of P-loop. Authors: Gong, X. / Chen, X. / Yu, D. / Zhang, N. / Zhu, Z. / Niu, L. / Mao, Y. / Ge, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.9 KB | Display | ![]() |
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PDB format | ![]() | 40.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.8 KB | Display | ![]() |
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Full document | ![]() | 446.1 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ttpC ![]() 4ttqC ![]() 1jjvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 24633.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: coaE, lpg1467 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-BU2 / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.5 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop Details: 0.23 M ammonium citrate dibasic, 17.5%(w/v) PEG 3350, 0.01 M ATP, 5%(v/v) 1,3-butanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→22.76 Å / Num. obs: 12710 / % possible obs: 84.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 4.6 / % possible all: 82.4 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 1jjv Resolution: 2.1→22.721 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→22.721 Å
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Refine LS restraints |
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LS refinement shell |
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