+Open data
-Basic information
Entry | Database: PDB / ID: 1yfg | ||||||
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Title | YEAST INITIATOR TRNA | ||||||
Components | YEAST INITIATOR TRNA | ||||||
Keywords | T-RNA / AMINO ACID TRANSPORT / TRANSFER RIBONUCLEIC ACID | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å | ||||||
Authors | Basavappa, 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 |
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Remark 999 | SEQUENCE 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". |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yfg.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yfg.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 1yfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yfg_validation.pdf.gz | 346.4 KB | Display | wwPDB validaton report |
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Full document | 1yfg_full_validation.pdf.gz | 390.2 KB | Display | |
Data in XML | 1yfg_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 1yfg_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/1yfg ftp://data.pdbj.org/pub/pdb/validation_reports/yf/1yfg | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 8 |
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-Sample preparation
Crystal | Density 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. | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 301 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 301.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS Density % sol: 82 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Details: Johnson, C.D., (1970) Nature, 226, 1246. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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.
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Displacement parameters | Biso mean: 33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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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 |