+Open data
-Basic information
Entry | Database: PDB / ID: 1ltq | ||||||
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Title | CRYSTAL STRUCTURE OF T4 POLYNUCLEOTIDE KINASE | ||||||
Components | POLYNUCLEOTIDE KINASEPolynucleotide 5'-hydroxyl-kinase | ||||||
Keywords | TRANSFERASE / KINASE / PHOSPHATASE / ALPHA/BETA / P-LOOP | ||||||
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 / SAD / Resolution: 2.33 Å | ||||||
Authors | Galburt, E.A. / Pelletier, J. / Wilson, G. / Stoddard, B.L. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase. Authors: Galburt, E.A. / Pelletier, J. / Wilson, G. / Stoddard, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ltq.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ltq.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ltq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/1ltq ftp://data.pdbj.org/pub/pdb/validation_reports/lt/1ltq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35234.594 Da / Num. of mol.: 1 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 / Production host: Escherichia coli (E. coli) References: UniProt: P06855, polynucleotide 5'-hydroxyl-kinase |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-DMS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.06 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97873 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2002 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97873 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 38288 / Num. obs: 38288 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 5.7 / % possible all: 97.7 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Num. measured all: 191084 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 97.7 % / Rmerge(I) obs: 0.288 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.33→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→50 Å
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Refinement | *PLUS Rfactor all: 0.238 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.236 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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