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Yorodumi- PDB-5x8a: Crystal structure of ATP bound thymidylate kinase from thermus th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x8a | ||||||
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Title | Crystal structure of ATP bound thymidylate kinase from thermus thermophilus HB8 | ||||||
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: 2.51 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 | 5x8a.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x8a.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 5x8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x8a_validation.pdf.gz | 784.2 KB | Display | wwPDB validaton report |
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Full document | 5x8a_full_validation.pdf.gz | 785.5 KB | Display | |
Data in XML | 5x8a_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5x8a_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/5x8a ftp://data.pdbj.org/pub/pdb/validation_reports/x8/5x8a | HTTPS FTP |
-Related structure data
Related structure data | 5x86C 5x8bC 5x8cC 5x8dC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 22009.543 Da / Num. of mol.: 2 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 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHX3, dTMP kinase |
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-Non-polymers , 5 types, 82 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-ATP / | #5: Chemical | #6: 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: 2.3 Å3/Da / Density % sol: 45.1 % |
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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 ULTRAX 18 / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→28.43 Å / Num. obs: 13363 / % possible obs: 95.3 % / Redundancy: 6.5 % / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.51→2.61 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X7J Resolution: 2.51→28.43 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.878 / SU B: 10.389 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 1.508 / ESU R Free: 0.331 / 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: 27.262 Å2
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Refinement step | Cycle: 1 / Resolution: 2.51→28.43 Å
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Refine LS restraints |
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