+Open data
-Basic information
Entry | Database: PDB / ID: 4r78 | ||||||
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Title | Crystal structure of LicA in complex with AMP | ||||||
Components | Choline kinase | ||||||
Keywords | TRANSFERASE / protein kinase-like fold | ||||||
Function / homology | Function and homology information choline kinase activity / kinase activity / phosphorylation / nucleotide binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Wang, L. / Jiang, Y.L. / Zhou, C.Z. / Chen, Y.X. | ||||||
Citation | Journal: Plos One / Year: 2015 Title: Structural and enzymatic characterization of the choline kinase LicA from Streptococcus pneumoniae Authors: Wang, L. / Jiang, Y.L. / Zhang, J.R. / Zhou, C.Z. / Chen, Y.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r78.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r78.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 4r78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/4r78 ftp://data.pdbj.org/pub/pdb/validation_reports/r7/4r78 | HTTPS FTP |
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-Related 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: 35610.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: licA / Production host: Escherichia coli (E. coli) References: UniProt: Q93MI3, UniProt: Q8DPI4*PLUS, choline kinase |
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#2: Chemical | ChemComp-MES / |
#3: Chemical | ChemComp-AMP / |
#4: 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: 1.89 Å3/Da / Density % sol: 34.96 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 30% PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97924 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 47856 / Num. obs: 47856 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 1.979 / Rsym value: 0.651 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→46.39 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.286 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.077 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.347 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→46.39 Å
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