+Open data
-Basic information
Entry | Database: PDB / ID: 5x8d | ||||||
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Title | D90L mutant of thermus thermophilus HB8 thymidylate kinase | ||||||
Components | Thymidylate kinase | ||||||
Keywords | TRANSFERASE / Nucleotide monophosphate kinase | ||||||
Function / homology | Function and homology information dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Chaudhary, S.K. / Jeyakanthan, J. / Sekar, K. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Structural and functional roles of dynamically correlated residues in thymidylate kinase. Authors: Chaudhary, S.K. / Jeyakanthan, J. / Sekar, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x8d.cif.gz | 85.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x8d.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 5x8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x8d_validation.pdf.gz | 450 KB | Display | wwPDB validaton report |
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Full document | 5x8d_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 5x8d_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 5x8d_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/5x8d ftp://data.pdbj.org/pub/pdb/validation_reports/x8/5x8d | HTTPS FTP |
-Related structure data
Related structure data | 5x86C 5x8aC 5x8bC 5x8cC 5x8jC 5x8kC 5x8vC 5x98C 5x99C 5xakC 5xalC 5xt8C 5x7jS 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: 22007.613 Da / Num. of mol.: 2 / Mutation: D90L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: tmk, TTHA1607 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHX3, dTMP kinase #2: Chemical | ChemComp-MG / #3: Chemical | #4: 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: 2.1 Å3/Da / Density % sol: 36.1 % |
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Crystal grow | Temperature: 295 K / Method: microbatch Details: 0.2M MgCl2.6H2O, 0.1 M Tris hydrochloride, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→76.64 Å / Num. obs: 15291 / % possible obs: 91.9 % / Redundancy: 7.9 % / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.26→2.33 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X7J Resolution: 2.26→76.64 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.543 / ESU R Free: 0.281 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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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 max: 68.42 Å2 / Biso mean: 21.8676 Å2 / Biso min: 6.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→76.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.259→2.318 Å / Total num. of bins used: 20
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