+Open data
-Basic information
Entry | Database: PDB / ID: 1ly1 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure and Mechanism of T4 Polynucleotide Kinase | ||||||
Components | polynucleotide kinase | ||||||
Keywords | TRANSFERASE / PNK / KINASE / PHOSPHATASE / POLYNUCLEOTIDE / T4 / PHAGE | ||||||
Function / homology | Function and homology information deoxynucleotide 3'-phosphatase / deoxynucleotide 3'-phosphatase activity / polynucleotide 5'-hydroxyl-kinase / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / phosphorylation / DNA repair / ATP binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2 Å | ||||||
Authors | Wang, L.K. / Lima, C.D. / Shuman, S. | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme. Authors: Wang, L.K. / Lima, C.D. / Shuman, S. | ||||||
History |
| ||||||
Remark 600 | HETEROGEN The sulfate ions mimic substrate nucleotide phosphates. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ly1.cif.gz | 46.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ly1.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 1ly1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ly1_validation.pdf.gz | 438 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ly1_full_validation.pdf.gz | 439 KB | Display | |
Data in XML | 1ly1_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1ly1_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/1ly1 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/1ly1 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20670.787 Da / Num. of mol.: 1 / Fragment: kinase domain, residues 1-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: PSET / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 References: UniProt: P06855, polynucleotide 5'-hydroxyl-kinase | ||
---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.01 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M NaOAc 4.6, 5mM DTT, 16% PEG2000MME, 0.4M AMSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 15, 2001 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 14453 / Num. obs: 12892 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2→2.06 Å / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.3 / % possible all: 77.7 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. measured all: 36111 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 77.7 % / Rmerge(I) obs: 0.223 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIR / Resolution: 2→19.01 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.5142 Å2 / ksol: 0.38958 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.22 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.01 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.277 / Rfactor Rwork: 0.278 |