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- PDB-1yfg: YEAST INITIATOR TRNA -

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Basic information

Entry
Database: PDB / ID: 1yfg
TitleYEAST INITIATOR TRNA
ComponentsYEAST INITIATOR TRNA
KeywordsT-RNA / AMINO ACID TRANSPORT / TRANSFER RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsBasavappa, R. / Sigler, P.B.
Citation
Journal: EMBO J. / Year: 1991
Title: The 3 A crystal structure of yeast initiator tRNA: functional implications in initiator/elongator discrimination.
Authors: Basavappa, R. / Sigler, P.B.
#1: Journal: Nature / Year: 1979
Title: Crystal Structure of a Eukaryotic Initiator tRNA
Authors: Schevitz, R.W. / Podjarny, A.D. / Krishnamachari, N. / Hughes, J.J. / Sigler, P.B. / Sussman, J.L.
History
DepositionMay 8, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Sep 3, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 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_validate_polymer_linkage / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE MOST OF THE MODEL IS CLEARLY DEFINED IN THE ELECTRON DENSITY MAPS. HOWEVER, PLEASE BE ...SEQUENCE MOST OF THE MODEL IS CLEARLY DEFINED IN THE ELECTRON DENSITY MAPS. HOWEVER, PLEASE BE AWARE THAT RESIDUES 29-41, COMPRISING MOST OF THE ANTICODON ARM, ARE HIGHLY DISORDERED.THE POSITIONS OF THESE RESIDUES ARE ONLY A BEST GUESS. IN PARTICULAR, THE ORIENTATION OF THE T6A MODIFICATION ON RESIDUE 37 IS VERY TENTATIVE. PLEASE USE CAUTION WHEN MAKING ANY SUPPOSITIONS BASED ON THE POSITIONS OF THESE RESIDUES. REFERENCE: IN ORDER TO ALIGN THE YEAST INITIATOR TRNA TO THE CANONICAL CLOVERLEAF NUMBERING SYSTEM, THERE IS NO RESIDUE NUMBERED "17".

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YEAST INITIATOR TRNA


Theoretical massNumber of molelcules
Total (without water)24,7141
Polymers24,7141
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)113.720, 113.720, 136.541
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: RNA chain YEAST INITIATOR TRNA


Mass: 24713.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 8

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Sample preparation

CrystalDensity Matthews: 5.16 Å3/Da / Density % sol: 82 %
Description: THE DATA QUALITY STATISTICS REPORTED ARE FOR THE COMBINED DATA SET FROM CHESS AND THE PHOTON FACTORY. THE MODEL SUBMITTED HERE IS BASED ON THE 4A STRUCTURE REPORTED IN REFERENCE 2 AND ...Description: THE DATA QUALITY STATISTICS REPORTED ARE FOR THE COMBINED DATA SET FROM CHESS AND THE PHOTON FACTORY. THE MODEL SUBMITTED HERE IS BASED ON THE 4A STRUCTURE REPORTED IN REFERENCE 2 AND REFINED AGAINST NEWLY COLLECTED DATA TO 3A.
Crystal growTemperature: 301 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 301.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NH4 SULFATE11
3MG SULFATE11
4SPERMINE11
5NA CACODYLATE11
Crystal
*PLUS
Density % sol: 82 %
Crystal grow
*PLUS
pH: 6 / Details: Johnson, C.D., (1970) Nature, 226, 1246.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.9 Mammonium sulfate1drop
20.005 M1dropMgCl2
30.005 Msodium cacodylate1drop
40.002 Mspermine HCl1drop
62.3 Mammonium sulfate1reservoir
5tRNA1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12781
22781
32781
Diffraction source
SourceSiteTypeID
SYNCHROTRONSSRL SSRL 1
SYNCHROTRONCHESS CHESS 2
SYNCHROTRONPhoton Factory PHOTON FACTORY 3
Detector
TypeIDDetectorDate
1FILMJan 1, 1988
KODAK2STORAGE PHOSPHORSJan 1, 1988
Y.AMEMIYA3IMAGE PLATEJan 1, 1988
Radiation
IDMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Mx-ray1
2Mx-ray2
3Mx-ray3
Radiation wavelength
IDRelative weight
11
21
31
ReflectionResolution: 3→20 Å / Num. obs: 10688 / % possible obs: 95 % / Observed criterion σ(I): 0 / Rsym value: 0.08 / Net I/σ(I): 15.7
Reflection shellResolution: 3→3.14 Å / Mean I/σ(I) obs: 2.24 / Rsym value: 0.495 / % possible all: 98.8
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.14 Å

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Processing

Software
NameVersionClassification
PHAREmodel building
DENMODmodel building
NUCLIN/PROFFTrefinement
MODIFIEDBY Z.OTWINOWSKIrefinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
NUCLINrefinement
PROFFT(MODIFIED BY Z.OTWINOWSKI)refinement
RefinementMethod to determine structure: MIR
Starting model: 4 A STRUCTURE REPORTED IN REFERENCE 2

Resolution: 3→10 Å / Cross valid method: NONE / σ(F): 1
Details: INDIVIDUAL ISOTROPIC TEMP. FACTOR RMS: 0.638. INDIVIDUAL ISOTROPIC TEMP. FACTOR SIGMA: 1.000. THE MODEL INITIALLY WAS REFINED AGAINST THE SSRL DATA USING NUCLIN/NUCLSQ AND THEN NUCLIN/PROFFT ...Details: INDIVIDUAL ISOTROPIC TEMP. FACTOR RMS: 0.638. INDIVIDUAL ISOTROPIC TEMP. FACTOR SIGMA: 1.000. THE MODEL INITIALLY WAS REFINED AGAINST THE SSRL DATA USING NUCLIN/NUCLSQ AND THEN NUCLIN/PROFFT HYBRID. FACTORY DATA AS THEY BECAME AVAILABLE. REFINEMENT PERFORMED WITH REFINEMENT CONTINUED AGAINST CHESS AND CHESS+PHOTON NUCLIN/PROFFT AND THEN X-PLOR. FINAL MODEL OBTAINED WITH NUCLIN/ PROFFT.
Rfactor% reflection
all0.215 -
obs-81.7 %
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1639 0 0 1639
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.025
X-RAY DIFFRACTIONp_angle_d0.0250.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0020.01
X-RAY DIFFRACTIONp_chiral_restr0.2470.3
X-RAY DIFFRACTIONp_singtor_nbd0.1150.2
X-RAY DIFFRACTIONp_multtor_nbd0.1680.638
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection obs: 8688 / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33 Å2

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