+Open data
-Basic information
Entry | Database: PDB / ID: 5x0b | ||||||
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Title | Free serine kinase in complex with AMP | ||||||
Components | Free serine kinase | ||||||
Keywords | TRANSFERASE / Thermococcus kodakarensis / cysteine biosynthesis | ||||||
Function / homology | Function and homology information L-serine kinase (ADP) / cysteine biosynthetic process / kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis KOD1 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Nagata, R. / Fujihashi, M. / Miki, K. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: Structural Study on the Reaction Mechanism of a Free Serine Kinase Involved in Cysteine Biosynthesis Authors: Nagata, R. / Fujihashi, M. / Kawamura, H. / Sato, T. / Fujita, T. / Atomi, H. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x0b.cif.gz | 110.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x0b.ent.gz | 82.4 KB | Display | PDB format |
PDBx/mmJSON format | 5x0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x0b_validation.pdf.gz | 737.6 KB | Display | wwPDB validaton report |
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Full document | 5x0b_full_validation.pdf.gz | 740.7 KB | Display | |
Data in XML | 5x0b_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 5x0b_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/5x0b ftp://data.pdbj.org/pub/pdb/validation_reports/x0/5x0b | HTTPS FTP |
-Related structure data
Related structure data | 5x0eC 5x0fC 5x0gC 5x0jC 5x0kC 1vk1S 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: 27739.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea) Strain: KOD1 / Gene: TK0378 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JD03 |
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#2: Chemical | ChemComp-AMP / |
#3: 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: 2.2 Å3/Da / Density % sol: 44.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 3350, serine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 25375 / % possible obs: 99.8 % / Redundancy: 6.7 % / Net I/σ(I): 16.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VK1 Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.327 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.128 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.812 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→50 Å
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Refine LS restraints |
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