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Yorodumi- PDB-2ia5: T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ia5 | ||||||
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Title | T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium. | ||||||
Components | Polynucleotide kinasePolynucleotide 5'-hydroxyl-kinase | ||||||
Keywords | TRANSFERASE / Polynucleotide Kinase Phosphatase Sulfate-Complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Zhu, H. / Smith, P.C. / Wang, L.K. / Lima, C.D. / Shuman, S. | ||||||
Citation | Journal: Virology / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ia5.cif.gz | 721.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ia5.ent.gz | 599.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ia5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/2ia5 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/2ia5 | HTTPS FTP |
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-Related structure data
Related structure data | 1ltqS S: Starting model for refinement |
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Similar structure data |
-Links
-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. |
-Components
#1: Protein | Mass: 34671.855 Da / Num. of mol.: 12 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: pET28-His10-Smt3 / 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-MG / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ARS / #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: 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: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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