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Yorodumi- PDB-1dd5: CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA RIBOSOME RECYCLING FACTO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dd5 | ||||||
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Title | CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA RIBOSOME RECYCLING FACTOR, RRF | ||||||
Components | RIBOSOME RECYCLING FACTOR | ||||||
Keywords | RIBOSOME / THREE-HELIX BUNDLE / BETA-ALPHA-BETA SANDWICH | ||||||
Function / homology | Function and homology information cytoplasmic translational termination / ribosomal large subunit binding / translation / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.55 Å | ||||||
Authors | Selmer, M. / Al-Karadaghi, S. / Hirokawa, G. / Kaji, A. / Liljas, A. | ||||||
Citation | Journal: Science / Year: 1999 Title: Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic. Authors: Selmer, M. / Al-Karadaghi, S. / Hirokawa, G. / Kaji, A. / Liljas, A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and Preliminary X-ray Analysis of Thermotoga Maritima Ribosome Recycling Factor Authors: Selmer, M. / Al-Karadaghi, S. / Hirokawa, G. / Kaji, A. / Liljas, A. #2: Journal: To be Published Title: Cloning and Overexpression of Thermotoga Maritima RRF Authors: Atarashi, K. / Kaji, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dd5.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dd5.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1dd5 ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1dd5 | HTTPS FTP |
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-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21548.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q9X1B9 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.5 Details: ammonium sulfate, acetate, glycerol , pH 5.5, VAPOR DIFFUSION, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||
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 | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.55→30 Å / Num. all: 11927 / Num. obs: 11648 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 27 | ||||||||||||||||||
Reflection shell | Resolution: 2.55→2.65 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 9.5 / Num. unique all: 1261 / % possible all: 91.8 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 91.8 % |
-Processing
Software |
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Refinement | Resolution: 2.55→30 Å / Rfactor Rfree error: 0.011 / Data cutoff high rms absF: 1478170 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Solved by selenomethionine MAD
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Solvent computation | Solvent model: flat model / Bsol: 23.6 Å2 / ksol: 0.331 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.8 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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