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- PDB-2ia5: T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium. -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ia5 | ||||||
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Title | T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium. | ||||||
![]() | Polynucleotide kinase | ||||||
![]() | TRANSFERASE / Polynucleotide Kinase Phosphatase Sulfate-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 | ![]() ![]() ![]() | ||||||
![]() | Zhu, H. / Smith, P.C. / Wang, L.K. / Lima, C.D. / Shuman, S. | ||||||
![]() | ![]() Title: Structure-function analysis of the 3' phosphatase component of T4 polynucleotide kinase/phosphatase. Authors: Zhu, H. / Smith, P. / Wang, L.K. / Shuman, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 721.1 KB | Display | ![]() |
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PDB format | ![]() | 599.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 554.6 KB | Display | ![]() |
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Full document | ![]() | 590.5 KB | Display | |
Data in XML | ![]() | 130.6 KB | Display | |
Data in CIF | ![]() | 174.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ltqS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | Biological unit is a homo-tetramer. The ASU contains three such tetramers. |
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Components
#1: Protein | Mass: 34671.855 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P06855, polynucleotide 5'-hydroxyl-kinase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ARS / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 100mM Sodium cacodylate, 12% PEG-8000, 0.2 M ammonium sulfate, 20 mM urea, 5 mM DTT, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2002 Details: Double crystal monochromator with sagitally focusing Si(111) crystals |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→40 Å / Num. all: 126336 / Num. obs: 124693 / % possible obs: 98.7 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -3 / Redundancy: 4.32 % / Biso Wilson estimate: 71.8 Å2 / Rsym value: 0.104 / Net I/σ(I): 12.01 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.57 / Num. unique all: 6245 / Rsym value: 0.535 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 1LTQ dimer Resolution: 2.9→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1948026.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: -0.445649 Å2 / ksol: 0.24 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→19.99 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
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Xplor file |
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