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Yorodumi- PDB-1rlg: Molecular basis of Box C/D RNA-protein interaction: co-crystal st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rlg | ||||||
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Title | Molecular basis of Box C/D RNA-protein interaction: co-crystal structure of the Archaeal sRNP intiation complex | ||||||
Components |
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Keywords | Structural Protein/RNA / PROTEIN-RNA / Structural Protein-RNA COMPLEX | ||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Moore, T. / Zhang, Y. / Fenley, M.O. / Li, H. | ||||||
Citation | Journal: STRUCTURE / Year: 2004 Title: Molecular Basis of Box C/D RNA-Protein Interactions; Cocrystal Structure of Archaeal L7Ae and a Box C/D RNA. Authors: Moore, T. / Zhang, Y. / Fenley, M.O. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rlg.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rlg.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 1rlg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/1rlg ftp://data.pdbj.org/pub/pdb/validation_reports/rl/1rlg | 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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2 |
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Unit cell |
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Details | The biological assembly is packed by a dimmer in the asymmetric unit by the operations of space group P23 |
-Components
#1: RNA chain | Mass: 8329.573 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 13212.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: RPL7AE, AF0764 / Plasmid: pET13 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O29494 |
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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: 3.66 Å3/Da / Density % sol: 66.12 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 303 K / Method: evaporation / pH: 7.5 Details: PEG 400,magnesium acetate, HEPES , pH 7.5, EVAPORATION, temperature 303K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 263 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.99, 1.09, 0.97 | ||||||||||||
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Apr 16, 2003 | ||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→29.25 Å / Num. obs: 30750 / % possible obs: 0.94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 80.7 Å2 | ||||||||||||
Reflection shell | Resolution: 2.7→2.71 Å / % possible all: 54 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→29.25 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 324127.19 / Data cutoff high rms absF: 324127.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.1653 Å2 / ksol: 0.290896 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→29.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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