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- PDB-1vtq: THREE-DIMENSIONAL STRUCTURE OF YEAST T-RNA-ASP. I. STRUCTURE DETE... -

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Entry
Database: PDB / ID: 1vtq
TitleTHREE-DIMENSIONAL STRUCTURE OF YEAST T-RNA-ASP. I. STRUCTURE DETERMINATION
ComponentsT-RNA-ASP
KeywordsRNA / T-RNA / SINGLE STRAND / LOOPS
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsComarmond, M.B. / Giege, R. / Thierry, J.C. / Moras, D. / Fischer, J.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1986
Title: Three-Dimensional Structure of Yeast T-RNA-ASP. I. Structure Determination
Authors: Comarmond, M.B. / Giege, R. / Thierry, J.C. / Moras, D. / Fischer, J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1986
Title: Anticodon-Anticodon Interaction Induces Conformational Changes in T-RNA. Yeast T-RNA-ASP II, a Model for T-RNA-M-RNA Recognition
Authors: Moras, D. / Dock, A.-C. / Dumas, P. / Westhof, E. / Romby, P. / Ebel, J.-P. / Giege, R.
#2: Journal: J.Mol.Biol. / Year: 1985
Title: Crystallographic Refinement of Yeast Aspartic Acid Transfer RNA
Authors: Westhof, E. / Dumas, P. / Moras, D.
#3: Journal: Biochimie / Year: 1985
Title: Crystal Structure of Yeast T-RNA-ASP. Atomic Coordinates
Authors: Dumas, P. / Ebel, J.P. / Giege, R. / Moras, D. / Thierry, J.C. / Westhof, E.
#4: Journal: J.Biomol.Struct.Dyn. / Year: 1983
Title: Loop Stereochemistry and Dynamics in Transfer RNA
Authors: Westhof, E. / Dumas, P. / Moras, D.
#5: Journal: Nature / Year: 1980
Title: Crystal Structure of Yeast T-RNA-ASP
Authors: Moras, D. / Comarmond, M.B. / Fischer, J. / Weiss, R. / Thierry, J.C. / Ebel, J.P. / Giege, R.
#6: Journal: J.Mol.Biol. / Year: 1977
Title: Yeast Transfer RNA-ASP. A New High-Resolution X-Ray Diffracting Crystal Form of a Transfer RNA
Authors: Giege, R. / Moras, D. / Thierry, J.C.
History
DepositionJun 11, 1985Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn / Item: _entity.pdbx_description / _entity.src_method
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-RNA-ASP


Theoretical massNumber of molelcules
Total (without water)24,1811
Polymers24,1811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.300, 68.000, 149.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: RNA chain T-RNA-ASP


Mass: 24181.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.18 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 3→10 Å / σ(F): 2
Details: TWO NON-ISOMORPHOUS INDEPENDENT CRYSTAL FORMS, REFERRED TO AS A FORM AND B FORM, HAVE BEEN GROWN AND SOLVED INDEPENDENTLY. THE COORDINATES PRESENTED IN THIS ENTRY ARE FOR THE B FORM.
RfactorNum. reflection
obs0.235 4585
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1602 0 0 1602

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