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Yorodumi- PDB-1evv: CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1evv | ||||||
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Title | CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION | ||||||
Components | PHENYLALANINE TRANSFER RNA | ||||||
Keywords | RNA / TRANSFER RNA / PHENYLALANINE / PHE-TRNA / YEAST / AMINO-ACID TRANSPORT | ||||||
Function / homology | SPERMINE / : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Saccharomyces (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Jovine, L. / Djordjevic, S. / Rhodes, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals. Authors: Jovine, L. / Djordjevic, S. / Rhodes, D. #1: Journal: J.Mol.Biol. / Year: 1972 Title: High-resolution X-ray diffraction studies on a pure species of transfer RNA Authors: Ladner, J.E. / Finch, J.T. / Klug, A. / Clark, B.F. #2: Journal: Nature / Year: 1974 Title: Structure of yeast phenylalanine tRNA at 3 A resolution Authors: Robertus, J.D. / Ladner, J.E. / Finch, J.T. / Rhodes, D. / Brown, R.S. / Clark, B.F.C. / Klug, A. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975 Title: Structure of yeast phenylalanine transfer RNA at 2.5 A resolution Authors: Ladner, J.E. / Jack, A. / Robertus, J.D. / Brown, R.S. / Rhodes, D. / Clark, B.F. / Klug, A. #4: Journal: J.Mol.Biol. / Year: 1978 Title: Further refinement of the structure of yeast tRNA Phe Authors: Hingerty, B. / Brown, R.S. / Jack, A. #5: 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. #6: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1evv.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1evv.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 1evv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1evv_validation.pdf.gz | 424.5 KB | Display | wwPDB validaton report |
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Full document | 1evv_full_validation.pdf.gz | 432.5 KB | Display | |
Data in XML | 1evv_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1evv_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/1evv ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1evv | HTTPS FTP |
-Related structure data
Related structure data | 1traS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 24890.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces (fungus) / Genus: Saccharomyces / References: GenBank: 176479 | ||||
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#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-SPM / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 59.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277.15 K / Method: dialysis / pH: 7.5 Details: CRYSTALS GROWN AT 277 K IN 0.010 M TRIS-HCL PH 7.5, 0.012 M MGCL2, 0.002 M SPERMINE, 6% 1,6-HEXANEDIOL. CRYOPROTECTION CONDITIONS: AFTER WASHING IN FRESH CRYSTALLIZATION SOLUTION FOR 10 MIN ...Details: CRYSTALS GROWN AT 277 K IN 0.010 M TRIS-HCL PH 7.5, 0.012 M MGCL2, 0.002 M SPERMINE, 6% 1,6-HEXANEDIOL. CRYOPROTECTION CONDITIONS: AFTER WASHING IN FRESH CRYSTALLIZATION SOLUTION FOR 10 MIN AND ADDITION OF 30% MPD (V/V), CRYSTALS WERE FLASH-FROZEN IN LIQUID NITROGEN, DIALYSIS, temperature 277.15K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932 |
Detector | Type: ADSC / Detector: CCD / Date: Apr 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 2→25.8 Å / Num. all: 13678 / Num. obs: 13678 / % possible obs: 88.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.036 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.171 / % possible all: 70.7 |
Reflection | *PLUS Num. measured all: 30638 / Rmerge(I) obs: 0.036 |
Reflection shell | *PLUS % possible obs: 70.7 % / Rmerge(I) obs: 0.171 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1TRA Resolution: 2→25.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 810557.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PARKINSON ET AL. Details: A LOW RESOLUTION LIMIT OF 6.O A WAS USED FOR INITIAL B FACTOR AND BULK SOLVENT CORRECTIONS. THE OCCUPANCY OF NUCLEOTIDE D16, AS WELL AS THOSE OF ATOMS P, O1P, O2P, O5* AND C5* OF NUCLEOTIDE ...Details: A LOW RESOLUTION LIMIT OF 6.O A WAS USED FOR INITIAL B FACTOR AND BULK SOLVENT CORRECTIONS. THE OCCUPANCY OF NUCLEOTIDE D16, AS WELL AS THOSE OF ATOMS P, O1P, O2P, O5* AND C5* OF NUCLEOTIDE D17, WERE REFINED TO ACCOUNT FOR MG2+-CATALYSED PARTIAL CLEAVAGE OF THE TRNA BACKBONE AT EITHER SIDE OF D16. DENSITY FOR THIS PART OF THE MOLECULE WAS POOR AND ITS PLACEMENT SHOULD THEREFORE BE CONSIDERED TENTATIVE. OCCUPANCIES OF ALL MG2+ IONS, THE SPERMINE AND ALL WATER MOLECULES WERE ALSO REFINED.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 113.1 Å2 / ksol: 0.468 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→25.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.11 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 7
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.413 / Rfactor Rwork: 0.34 |