[English] 日本語
Yorodumi- PDB-5xak: Crystal structure (form II) of thymidylate kinase from Thermus th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xak | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure (form II) of thymidylate kinase 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5xak.cif.gz | 159.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5xak.ent.gz | 124.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/5xak ftp://data.pdbj.org/pub/pdb/validation_reports/xa/5xak | HTTPS FTP |
---|
-Related structure data
Related structure data | 5x86C 5x8aC 5x8bC 5x8cC 5x8dC 5x8jC 5x8kC 5x8vC 5x98C 5x99C 5xalC 5xt8C 2pbrS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHX3, dTMP kinase #2: Chemical | #3: Chemical | ChemComp-CS / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 33.99 % |
---|---|
Crystal grow | Temperature: 295 K / Method: microbatch / Details: CsCl2.H2O, 30% PEG 3500 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9737 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9737 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25.16 Å / Num. obs: 53700 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 15.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.5→1.53 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PBR Resolution: 1.5→25.16 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.979 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.07 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.238 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.5→25.16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|