+Open data
-Basic information
Entry | Database: PDB / ID: 434d | ||||||
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Title | 5'-R(*UP*AP*GP*CP*UP*CP*C)-3', 5'-R(*GP*GP*GP*GP*CP*UP*A)-3' | ||||||
Components |
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Keywords | RNA / 7 BASE-PAIR TRNA ALA ACCEPTOR STEM / DOUBLE HELIX | ||||||
Function / homology | STRONTIUM ION / RNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.16 Å | ||||||
Authors | Mueller, U. / Schuebel, H. / Sprinzl, M. / Heinemann, U. | ||||||
Citation | Journal: RNA / Year: 1999 Title: Crystal structure of acceptor stem of tRNA(Ala) from Escherichia coli shows unique G.U wobble base pair at 1.16 A resolution. Authors: Mueller, U. / Schubel, H. / Sprinzl, M. / Heinemann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 434d.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb434d.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 434d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/34/434d ftp://data.pdbj.org/pub/pdb/validation_reports/34/434d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 2157.331 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: RNA chain | Mass: 2276.419 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-SR / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 21 ℃ | ||||||||||||||||||||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: X11 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 3, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.16→15 Å / Num. obs: 23758 / % possible obs: 88.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.16→1.17 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.5 / % possible all: 75.7 |
Reflection shell | *PLUS % possible obs: 75.7 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: CANONICAL A-FORM RNA Resolution: 1.16→15 Å / Num. parameters: 6691 / Num. restraintsaints: 20934 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: PARKINSON, G. ET AL.
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Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 739 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→15 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.155 / Rfactor Rfree: 0.18 / Rfactor Rwork: 0.124 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |