[English] 日本語
Yorodumi- PDB-1jj2: Fully Refined Crystal Structure of the Haloarcula marismortui Lar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jj2 | ||||||
---|---|---|---|---|---|---|---|
Title | Fully Refined Crystal Structure of the Haloarcula marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution | ||||||
Components |
| ||||||
Keywords | RIBOSOME / RIBOSOME ASSEMBLY / RNA-RNA / PROTEIN-RNA / PROTEIN-PROTEIN | ||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / mRNA splicing, via spliceosome / 5S rRNA binding / large ribosomal subunit rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / mRNA splicing, via spliceosome / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / DNA repair / mRNA binding / nucleotide binding / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Haloarcula marismortui (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Klein, D.J. / Schmeing, T.M. / Moore, P.B. / Steitz, T.A. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: The kink-turn: a new RNA secondary structure motif. Authors: Klein, D.J. / Schmeing, T.M. / Moore, P.B. / Steitz, T.A. #1: Journal: To be published Title: The Fully Refined Crystal Structure of the H. marismortui 50S Subunit at 2.4 Angstrom Resolution Authors: Klein, D.J. / Schmeing, T.M. / Nissen, P. / Ban, N. / Moore, P.B. / Steitz, T.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jj2.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jj2.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 1jj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jj2_validation.pdf.gz | 766.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jj2_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1jj2_validation.xml.gz | 314.9 KB | Display | |
Data in CIF | 1jj2_validation.cif.gz | 498.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/1jj2 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/1jj2 | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-RNA chain , 2 types, 2 molecules 09
#1: RNA chain | Mass: 946034.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779 |
---|---|
#2: RNA chain | Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779 |
+RIBOSOMAL PROTEIN ... , 28 types, 28 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ12
-Non-polymers , 6 types, 8125 molecules
#31: Chemical | ChemComp-MG / #32: Chemical | #33: Chemical | ChemComp-NA / #34: Chemical | ChemComp-CL / #35: Chemical | ChemComp-CD / #36: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.74 % | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG 6000, KCL, NH4CL, MGCL2, CDCL2, POTASSIUM ACETATE, TRIS-MES, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: data unknown | ||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||
Detector |
| |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 2.4→90 Å / Num. all: 666819 / Num. obs: 666819 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 26.6 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 6 % / Rmerge(I) obs: 0.691 / % possible all: 73.5 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 90 Å |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.189 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|