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- PDB-4tra: RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ... -

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Entry
Database: PDB / ID: 4tra
TitleRESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS
ComponentsTRNAPHE
KeywordsT-RNA / SINGLE STRAND / LOOPS
Function / homologyRNA / 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: J.Mol.Biol. / Year: 1978
Title: Crystal Structure of Yeast Phenylalanine T-RNA. I.Crystallographic Refinement
Authors: Sussman, J.L. / Holbrook, S.R. / Warrant, R.W. / Church, G.M. / Kim, S.-H.
#3: Journal: J.Mol.Biol. / Year: 1978
Title: Crystal Structure of Yeast Phenylalanine T-RNA. II.Structural Features and Functional Implications
Authors: Holbrook, S.R. / Sussman, J.L. / Warrant, R.W. / Kim, S.-H.
#4: Journal: Adv.Enzymol.Relat.Areas Mol.Biol. / Year: 1978
Title: Three Dimensional Structure of T-RNA and its Functional Implications
Authors: Kim, S.-H.
#5: Journal: Sci.Am. / Year: 1978
Title: The Three-Dimensional Structure of Transfer RNA
Authors: Rich, A. / Kim, S.H.
#6: Journal: Transfer RNA / Year: 1978
Title: Crystal Structure of Yeast Phenylalanine T-RNA, its Correlation to the Solution Structure and the Functional Implications
Authors: Kim, S.-H.
#7: Journal: Nucleic Acids Res. / Year: 1977
Title: RNA-Ligand Interactions. (1) Magnesium Binding Sites in Yeast T-RNA-PHE
Authors: Holbrook, S.R. / Sussman, J.L. / Warrant, R.W. / Church, G.M. / Kim, S.-H.
#8: Journal: Biochem.Biophys.Res.Commun. / Year: 1976
Title: Idealized Atomic Coordinates of Yeast Phenylalanine Transfer RNA
Authors: Sussman, J.L. / Kim, S.-H.
#9: Journal: Science / Year: 1976
Title: Three-dimensional Structure of a Transfer RNA in Two Crystal Forms
Authors: Sussman, J.L. / Kim, S.-H.
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: Non-polymer description / Version format compliance
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_struct_conn_angle / pdbx_validate_symm_contact / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _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.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.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
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation

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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
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.000, 56.000, 161.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal grow
*PLUS
Method: unknown

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 3→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.172 4508
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1652 4 123 1779
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.008
X-RAY DIFFRACTIONn_angle_d0.014
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 / Num. reflection all: 7244 / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.008
X-RAY DIFFRACTIONn_angle_d0.014

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