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- PDB-2tra: RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ... -

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Basic information

Entry
Database: PDB / ID: 2tra
TitleRESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS
ComponentsTRNAASP
KeywordsT-RNA / SINGLE STRAND / LOOPS
Function / homologySPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsWesthof, E. / Dumas, P. / Moras, D.
Citation
Journal: Acta Crystallogr.,Sect.A / Year: 1988
Title: Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals.
Authors: Westhof, E. / Dumas, P. / Moras, D.
#1: Journal: Biochimie / Year: 1988
Title: Hydration of Transfer RNA Molecules. A Crystallographic Study
Authors: Westhof, E. / Dumas, P. / Moras, D.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1986
Title: Thee-Dimensional Structure of Yeast T-RNA-ASP. I. Structure Determination
Authors: Comarmond, M.B. / Giege, R. / Thierry, J.C. / Moras, D. / Fischer, J.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1986
Title: Anticodon-Anticodon Interaction Induces Conformational Changes in T-RNA. Yeast T-RNA-ASP, 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.
#4: Journal: J.Mol.Biol. / Year: 1985
Title: Crystallographic Refinement of Yeast Aspartic Acid Transfer RNA
Authors: Westhof, E. / Dumas, P. / Moras, D.
#5: 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.
#6: Journal: J.Biomol.Struct.Dyn. / Year: 1983
Title: Loop Stereochemistry and Dynamics in Transfer RNA
Authors: Westhof, E. / Dumas, P. / Moras, D.
#7: 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.
#8: 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
DepositionNov 6, 1987Deposition site: BNL / Processing site: BNL
Revision 1.0Nov 6, 1987Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 22, 2016Group: Derived calculations
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / 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 / _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.pdbx_ptnr1_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRNAASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4083
Polymers24,1811
Non-polymers2272
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.500, 67.500, 149.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-124-

HOH

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Components

#1: RNA chain TRNAASP


Mass: 24181.369 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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal grow
*PLUS
Method: unknown

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 3→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.193 4335
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1560 15 94 1669
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.012
X-RAY DIFFRACTIONn_angle_d0.022
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.012
X-RAY DIFFRACTIONn_angle_d0.022

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