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Open data
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Basic information
Entry | Database: PDB / ID: 1rc8 | ||||||
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Title | T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA | ||||||
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![]() | TRANSFERASE/DNA / KINASE / PHOSPHATASE / ALPHA/BETA / P-LOOP / ssDNA / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Eastberg, J.H. / Pelletier, J. / Stoddard, B.L. | ||||||
![]() | ![]() Title: Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase. Authors: Eastberg, J.H. / Pelletier, J. / Stoddard, B.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.7 KB | Display | ![]() |
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PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 713.6 KB | Display | ![]() |
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Full document | ![]() | 723.4 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rpzC ![]() 1rrcC ![]() 1ltqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-DNA chain / Protein , 2 types, 2 molecules BA
#1: DNA chain | Mass: 1480.012 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 35234.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P06855, polynucleotide 5'-hydroxyl-kinase |
-Non-polymers , 4 types, 62 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-DMS / |
#5: Chemical | ChemComp-ADP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.64 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 4000, Potassium Chloride, MES, Tris, ATP, DTT, EDTA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging drop / Details: Galburt, E.A., (2002) Structure, 10, 1249. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 2002 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. all: 11117 / Num. obs: 11117 / % possible obs: 89.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.75→2.85 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 5 / % possible all: 91.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Redundancy: 5-6 / Num. measured all: 92826 |
Reflection shell | *PLUS % possible obs: 91.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LTQ Resolution: 2.75→38.19 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 161032.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.4922 Å2 / ksol: 0.328913 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→38.19 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.75 Å / Total num. of bins used: 6 /
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Xplor file |
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Refinement | *PLUS Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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