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Yorodumi- PDB-4ttp: Crystal structure of Legionella pneumophila dephospho-CoA kinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ttp | |||||||||
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Title | Crystal structure of Legionella pneumophila dephospho-CoA kinase in apo-form | |||||||||
Components | Dephospho-CoA kinase | |||||||||
Keywords | TRANSFERASE / kinase / P-loop / Coenzyme metabolism | |||||||||
Function / homology | Function and homology information dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Gong, X. / Ge, H. | |||||||||
Funding support | China, 2items
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Citation | Journal: J.Struct.Biol. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ttp.cif.gz | 57 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ttp.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ttp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ttp_validation.pdf.gz | 421.6 KB | Display | wwPDB validaton report |
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Full document | 4ttp_full_validation.pdf.gz | 423.7 KB | Display | |
Data in XML | 4ttp_validation.xml.gz | 10 KB | Display | |
Data in CIF | 4ttp_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/4ttp ftp://data.pdbj.org/pub/pdb/validation_reports/tt/4ttp | HTTPS FTP |
-Related structure data
Related structure data | 4ttqC 4ttrSC C: citing same article (ref.) 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: 24633.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: coaE, lpg1467 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q5ZVH3, dephospho-CoA kinase |
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#2: 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: 2.6 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M Sodium citrate (pH 5.6), 12%(w/v) PEG4000, 18%(v/v) 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 12960 / % possible obs: 96.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 5.2 / % possible all: 97.9 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TTR Resolution: 2.2→33.898 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.27 / 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: 2.2→33.898 Å
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Refine LS restraints |
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LS refinement shell |
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