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Yorodumi- PDB-1kqs: The Haloarcula marismortui 50S Complexed with a Pretranslocationa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kqs | |||||||||
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Title | The Haloarcula marismortui 50S Complexed with a Pretranslocational Intermediate in Protein Synthesis | |||||||||
Components |
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Keywords | RIBOSOME / RIBOSOME ASSEMBLY / RNA-RNA / PROTEIN-RNA / PROTEIN-PROTEIN / PROTEIN SYNTHESIS / PEPTIDYL TRANSFERASE | |||||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | Haloarcula marismortui (Halophile) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å | |||||||||
Authors | Schmeing, T.M. / Seila, A.C. / Hansen, J.L. / Freeborn, B. / Soukup, J.K. / Scaringe, S.A. / Strobel, S.A. / Moore, P.B. / Steitz, T.A. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits. Authors: Schmeing, T.M. / Seila, A.C. / Hansen, J.L. / Freeborn, B. / Soukup, J.K. / Scaringe, S.A. / Strobel, S.A. / Moore, P.B. / Steitz, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kqs.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1kqs.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 1kqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kqs_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1kqs_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1kqs_validation.xml.gz | 326.6 KB | Display | |
Data in CIF | 1kqs_validation.cif.gz | 513 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/1kqs ftp://data.pdbj.org/pub/pdb/validation_reports/kq/1kqs | HTTPS FTP |
-Related structure data
Related structure data | |
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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
-RNA chain , 4 types, 4 molecules 0934
#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 |
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#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 |
#3: RNA chain | Mass: 894.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid phase synthesis |
#4: RNA chain | Mass: 565.406 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Solid phase synthesis, followed by peptidyl transferase reaction. |
+RIBOSOMAL PROTEIN ... , 28 types, 28 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ12
-Non-polymers , 10 types, 8107 molecules
#33: Chemical | ChemComp-MG / #34: Chemical | #35: Chemical | ChemComp-NA / #36: Chemical | ChemComp-CL / #37: Chemical | ChemComp-PPU / | #38: Chemical | ChemComp-PHA / | #39: Chemical | ChemComp-ACA / | #40: Chemical | ChemComp-BTN / | #41: Chemical | ChemComp-CD / #42: 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: 3.16 Å3/Da / Density % sol: 61.07 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 6000, KCl, NH4Cl, MgCl2, CdCl2, POTASSIUM ACETATE, TRIS-MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: unknown / Details: data unknown | ||||||||||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 1.033 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Sep 29, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.07→45 Å / Num. all: 2581688 / Num. obs: 2581688 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 3.07→3.15 Å / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 45 Å / Num. obs: 340617 / Redundancy: 7.6 % / Num. measured all: 2581688 |
Reflection shell | *PLUS % possible obs: 99.7 % / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 3.1→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.12 Å / Num. reflection Rfree: 57 | ||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.1709 / Rfactor Rfree: 0.2205 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3.07 Å / Lowest resolution: 3.15 Å |