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- PDB-1tn1: CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CA... -

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Basic information

Entry
Database: PDB / ID: 1tn1
TitleCRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA
ComponentsTRNAPHE
KeywordsRNA / TRANSLATION
Function / homologyLEAD (II) ION / SPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsDewan, J.C. / Brown, R.S. / Hingerty, B.E. / 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 tRNA-Phe-Implications for Lead Toxicity and Self-Splicing RNA
Authors: Brown, R.S. / Hingerty, B.E. / Dewan, J.C. / Klug, A.
History
DepositionDec 4, 1986Processing site: BNL
Revision 1.0Jan 15, 1987Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Other / Version format compliance
Revision 1.3May 25, 2016Group: Source and taxonomy
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.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_asym_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_asym_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
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn

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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
Nonpolymer detailsPB(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 COORDINATION SITES FOR THE PB IONS COULD NOT BE FULLY CHARACTERIZED BECAUSE OF DIFFICULTIES IN ASSIGNING BOUND WATER LIGANDS AT 3.0 ANGSTROMS RESOLUTION. A DESCRIPTION OF THE INTERACTION REGIONS IS GIVEN IN REFERENCE 1 ABOVE.

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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

RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 4821 / Num. measured all: 10704

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor 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 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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