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- PDB-4tna: FURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHE -

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Basic information

Entry
Database: PDB / ID: 4tna
TitleFURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHE
ComponentsTRNAPHE
KeywordsT-RNA / SINGLE STRAND / LOOPS
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHingerty, B.E. / Brown, R.S. / Jack, A.
Citation
Journal: J.Mol.Biol. / Year: 1978
Title: Further refinement of the structure of yeast tRNAPhe.
Authors: Hingerty, B. / Brown, R.S. / Jack, A.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1978
Title: Refinement of Large Structures by Simultaneous Minimization of Energy and R Factor
Authors: Jack, A. / Levitt, M.
#2: Journal: J.Mol.Biol. / Year: 1977
Title: A Crystallographic Study of Metal-Binding to Yeast Phenylalanine Transfer RNA
Authors: Jack, A. / Ladner, J.E. / Rhodes, D. / Brown, R.S. / Klug, A.
#3: Journal: J.Mol.Biol. / Year: 1976
Title: Crystallographic Refinement of Yeast Phenylalanine Transfer RNA at 2.5 Angstroms Resolution
Authors: Jack, A. / Ladner, J.E. / Klug, A.
#4: Journal: Nucleic Acids Res. / Year: 1975
Title: Atomic Coordinates for Yeast Phenylalanine T-RNA
Authors: Ladner, J.E. / Jack, A. / Robertus, J.D. / Brown, R.S. / Rhodes, D. / Clark, B.F.C. / Klug, A.
#5: Journal: Nature / Year: 1974
Title: Structure of Yeast Phenylalanine T-RNA at 3 Angstroms Resolution
Authors: Robertus, J.D. / Ladner, J.E. / Finch, J.T. / Rhodes, D. / Brown, R.S. / Clark, B.F.C. / Klug, A.
#6: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionApr 12, 1978Deposition site: BNL / Processing site: BNL
Revision 1.0Apr 12, 1978Provider: repository / Type: Initial release
SupersessionMay 17, 1978ID: 3TNA
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)24,9875
Polymers24,8901
Non-polymers974
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.300, 33.400, 63.000
Angle α, β, γ (deg.)90.00, 90.25, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 48.31 %
Crystal grow
*PLUS
Method: other / Details: Jack, A., (1976) J. Mol. Biol., 108, 619.

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 8006 / Rmerge(I) obs: 0.057

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Processing

SoftwareName: JACK-LEVITT / Classification: refinement
RefinementHighest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1652 4 0 1656
Refinement
*PLUS
Highest resolution: 2.5 Å / Num. reflection obs: 8006 / Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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