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- PDB-1tn1: CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tn1 | ||||||
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Title | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA | ||||||
![]() | TRNAPHE | ||||||
![]() | RNA / TRANSLATION | ||||||
Function / homology | LEAD (II) ION / SPERMINE / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Dewan, J.C. / Brown, R.S. / Hingerty, B.E. / Klug, A. | ||||||
![]() | ![]() Title: Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA. Authors: Brown, R.S. / Dewan, J.C. / Klug, A. #1: ![]() Title: Pb(II)-Catalysed Cleavage of the Sugar-Phosphate Backbone of Yeast tRNA-Phe-Implications for Lead Toxicity and Self-Splicing RNA Authors: Brown, R.S. / Hingerty, B.E. / Dewan, J.C. / Klug, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69 KB | Display | ![]() |
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PDB format | ![]() | 41.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 362.7 KB | Display | ![]() |
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Full document | ![]() | 453.2 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: RNA chain | Mass: 24890.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
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#2: Chemical | ChemComp-SPM / | ||||||
#3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | PB(1) IS BOUND IN THE T-PSI-C LOOP. PB(2) IS BOUND IN THE EXTRA LOOP REGION. PB(3) IS BOUND IN THE ...PB(1) IS BOUND IN THE T-PSI-C LOOP. PB(2) IS BOUND IN THE EXTRA LOOP REGION. PB(3) IS BOUND IN THE ANTICODON LOOP. THE COORDINATI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.37 % |
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-Data collection
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 4821 / Num. measured all: 10704 |
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Processing
Software | Name: EREF / Classification: refinement | ||||||||||||
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Refinement | Rfactor Rwork: 0.227 / Highest resolution: 3 Å Details: AT PRESENT THE COORDINATES FOR THE PH7.4 PB-TRNA ARE NOT AVAILABLE. THUS ONLY THE COORDINATES FOR THE PB IONS ARE INCLUDED IN THIS ENTRY. REFINEMENT OF THE PH5.0 AND PH7.4 STRUCTURES ...Details: AT PRESENT THE COORDINATES FOR THE PH7.4 PB-TRNA ARE NOT AVAILABLE. THUS ONLY THE COORDINATES FOR THE PB IONS ARE INCLUDED IN THIS ENTRY. REFINEMENT OF THE PH5.0 AND PH7.4 STRUCTURES INDICATED THAT THEY CHANGED VERY LITTLE FROM THE NATIVE STRUCTURE. THE ONLY REAL DIFFERENCE IS THE PRESENCE OF THE PB IONS. ALSO, IN THE PH 7.4 STRUCTURE, THE SUGAR-PHOSPHATE BACKBONE IS CLEAVED BETWEEN RESIDUES H2U 17 AND G 18. THIS ENTRY ORIGINALLY CONTAINED ONLY THE COORDINATES OF THE THREE PB IONS. IN ORDER TO BRING COMPLETENESS TO THE STRUCTURE, THE ENTRY HAS BEEN REMEDIATED BY MERGING THE COORDINATES OF THE TRNA, MG ION AND WATER FROM THE RELATED ENTRY 1TN2. | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3 Å
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Refinement | *PLUS Highest resolution: 3 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |