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- PDB-1tra: RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANI... -

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Basic information

Entry
Database: PDB / ID: 1tra
TitleRESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES
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. / Sundaralingam, M.
Citation
Journal: Biochemistry / Year: 1986
Title: Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles.
Authors: Westhof, E. / Sundaralingam, M.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1978
Title: Crystal and Molecular Structure of Yeast Phenylalanyl Transfer RNA. Structure Determination, Difference Fourier Refinement, Molecular Conformation, Metal and Solvent Binding
Authors: Stout, C.D. / Mizuno, H. / Rao, S.T. / Swaminathan, P. / Rubin, J. / Brennan, T. / Sundaralingam, M.
#2: Journal: Nucleic Acids Res. / Year: 1976
Title: Atomic Coordinates and Molecular Conformation of Yeast Phenylalanyl T-RNA, an Independent Investigation
Authors: Stout, C.D. / Mizuno, H. / Rubin, J. / Brennan, T. / Rao, S.T. / Sundaralingam, M.
#3: Journal: Nucleic Acids Res. / Year: 1976
Title: Mechanisms of Chain Folding in Nucleic Acids, the (Omega,Omega) Plot and Its Correlation to the Nucleotide Geometry in Yeast T-RNA(PHE)
Authors: Sundaralingam, M. / Mizuno, H. / Stout, C.D. / Rao, S.T. / Liebman, M. / Yathindra, N.
#4: Journal: Nature New Biol. / Year: 1972
Title: X-Ray Diffraction Study of a New Crystal Form of Yeast Phenylalanine T-RNA
Authors: Ichikawa, T. / Sundaralingam, M.
#5: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionMay 16, 1986Deposition site: BNL / Processing site: BNL
SupersessionJul 14, 1986ID: 8TNA
Revision 1.0Jul 14, 1986Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 27, 2011Group: Other
Revision 1.4Feb 14, 2024Group: 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 / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRNAPHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0126
Polymers24,8901
Non-polymers1225
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.000, 33.300, 63.000
Angle α, β, γ (deg.)90.00, 90.40, 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.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal grow
*PLUS
Method: other
Details: Ichikawa, T., (1972) Nature New Biol., 236, 174., Ladner, J.E., (1972) J. Mol. Biol., 72, 99.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. obs: 4019 / Observed criterion σ(I): 3

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 3 Å /
RfactorNum. reflection
obs0.168 4019
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1652 5 110 1767
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.008
X-RAY DIFFRACTIONn_angle_d0.015
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

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