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Yorodumi- PDB-5xt8: Magnesium bound apo structure of thymidylate kinase (form I) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xt8 | ||||||
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Title | Magnesium bound apo structure of thymidylate kinase (form I) from Thermus thermophilus HB8 | ||||||
Components | Thymidylate kinase | ||||||
Keywords | TRANSFERASE / Nucleotide monophosphate kinase | ||||||
Function / homology | Function and homology information dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 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 | 5xt8.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xt8.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/5xt8 ftp://data.pdbj.org/pub/pdb/validation_reports/xt/5xt8 | HTTPS FTP |
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-Related structure data
Related structure data | 5x86C 5x8aC 5x8bC 5x8cC 5x8dC 5x8jC 5x8kC 5x8vC 5x98C 5x99C 5xakC 5xalC 5x7jS S: Starting model for refinement C: citing same article (ref.) |
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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: 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 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q5SHX3, dTMP kinase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Chemical | #5: 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: 2.2 Å3/Da / Density % sol: 44.8 % |
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Crystal grow | Temperature: 295 K / Method: microbatch Details: 0.2M MgCl2.6H2O, 0.1M 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: 1.541 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.87 Å / Num. obs: 26844 / % possible obs: 97.2 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2→2.05 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X7J Resolution: 2.01→48.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.163 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 95.3 Å2 / Biso mean: 23.2332 Å2 / Biso min: 9.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→48.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.062 Å / Total num. of bins used: 20
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