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Yorodumi- PDB-1l9a: CRYSTAL STRUCTURE OF SRP19 IN COMPLEX WITH THE S DOMAIN OF SIGNAL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l9a | ||||||
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Title | CRYSTAL STRUCTURE OF SRP19 IN COMPLEX WITH THE S DOMAIN OF SIGNAL RECOGNITION PARTICLE RNA | ||||||
Components |
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Keywords | SIGNALING PROTEIN/RNA / PROTEIN-RNA COMPLEX / RIBONUCLEOPROTEIN / SRP / SIGNAL RECOGNITION PARTICLE / TETRALOOP / SIGNALING PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Oubridge, C. / Kuglstatter, A. / Jovine, L. / Nagai, K. | ||||||
Citation | Journal: Mol.Cell / Year: 2002 Title: Crystal structure of SRP19 in complex with the S domain of SRP RNA and its implication for the assembly of the signal recognition particle. Authors: Oubridge, C. / Kuglstatter, A. / Jovine, L. / Nagai, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l9a.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l9a.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 1l9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/1l9a ftp://data.pdbj.org/pub/pdb/validation_reports/l9/1l9a | 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
#1: RNA chain | Mass: 41566.715 Da / Num. of mol.: 1 / Mutation: C112G, G113A, G238U, G239C / Source method: obtained synthetically Details: This sequence is 7SL RNA from Homo sapiens. 128 nt RNA fragment was in vitro transcribed under control of a T7 promoter with T7 RNA polymerase. It was Cotranscribed with 2 cis-acting ...Details: This sequence is 7SL RNA from Homo sapiens. 128 nt RNA fragment was in vitro transcribed under control of a T7 promoter with T7 RNA polymerase. It was Cotranscribed with 2 cis-acting hammerhead ribozymes to cleave homogeneous RNA from the full length transcript. References: GenBank: 23932 | ||||
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#2: Protein | Mass: 10341.349 Da / Num. of mol.: 1 / Mutation: C61A, C63R, C80A, Q74C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: SRP19 / Plasmid: pRET3a / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q58440 | ||||
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-MMC / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.9 % Description: ORIGINAL PHASES WERE DETERMINED BY SELENOMETHIONINE MAD BUT FINAL REFINEMENT WAS CARRIED OUT AGAINST A HIGHER QUALITY SINGLE WAVELENGTH DATASET FOR WHICH WE SUPPLY STATISTICS. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300.5 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 12% PEG4000, 110MM Tris.HCl pH 7.4, 10% glycerol, 50mm magnesium acetate, 100MM ammonium acetate, 5MM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 300.5K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 27.5 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: BM14 / Wavelength: 0.9185 / Wavelength: 0.9185 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 30, 2001 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9185 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→38 Å / Num. all: 29278 / Num. obs: 26760 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 114.6 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.1 / % possible all: 52.9 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 38 Å / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS % possible obs: 52.9 % / Num. possible: 1544 / Rmerge(I) obs: 0.31 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→37.84 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 427207.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS/Refmac Dictionaries / Details: Refmac5.1 (Murshudov) was also used in refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.92 Å2 / ksol: 0.282066 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 98.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→37.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.12 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 5
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.264 / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.264 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.419 / Rfactor Rwork: 0.375 |