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- PDB-1tn2: CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CA... -

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Basic information

Entry
Database: PDB / ID: 1tn2
TitleCRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNA
ComponentsTRNAPHE
KeywordsT-RNA / SINGLE STRAND / LOOPS
Function / homologyLEAD (II) ION / SPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsBrown, R.S. / Dewan, J.C. / Klug, A.
Citation
Journal: Biochemistry / Year: 1985
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: Journal: Nature / Year: 1983
Title: Pb(II)-Catalysed Cleavage of the Sugar-Phosphate Backbone of Yeast T-RNA-PHE-Implications for Lead Toxicity and Self-Splicing RNA
Authors: Brown, R.S. / Hingerty, B.E. / Dewan, J.C. / Klug, A.
History
DepositionAug 22, 1986Deposition site: BNL / Processing site: BNL
Revision 1.0Oct 24, 1986Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRNAPHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,83610
Polymers24,8901
Non-polymers9459
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.700, 33.200, 63.000
Angle α, β, γ (deg.)90.00, 89.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain TRNAPHE


Mass: 24890.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pb
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.37 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 4893 / Num. measured all: 10778

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Processing

SoftwareName: JACK-LEVITT / Classification: refinement
RefinementRfactor obs: 0.237 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1652 22 107 1781
Refinement
*PLUS
Highest resolution: 3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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