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Yorodumi- PDB-483d: CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 483d | ||||||
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Title | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | ||||||
Components | SARCIN/RICIN RRNA DOMAIN | ||||||
Keywords | RNA / SACIN/RICIN DOMAIN RNA RECOGNITION RIBOSOMES ELONGATION FACTORS CRYSTAL STRUCTURE | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å | ||||||
Authors | Correll, C.C. / Wool, I.G. / Munishkin, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: the structure at 1.11 A resolution. Authors: Correll, C.C. / Wool, I.G. / Munishkin, A. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Crystal Structure of the Ribosomal RNA Domain Essential for Binding Elongation Factors Authors: Correll, C.C. / Munishkin, A. / Chan, Y.-L. / Ren, Z. / Wool, I.G. #2: Journal: Biophys.J. / Year: 1999 Title: Comparison of the Crystal and Solution Structures of Two RNA Oligonucleotides Authors: Rife, J.P. / Stallings, S.G. / Correll, C.C. / Dallas, A. / Steitz, T.A. / Moore, P.B. #3: Journal: J.Mol.Biol. / Year: 1995 Title: The Sarcin/Ricin Loop, a Modular RNA Authors: Szewczak, A.A. / Moore, P.B. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: The Conformation of the Sarcin/Ricin Loop from 28 S Ribosomal RNA Authors: Szewczak, A.A. / Moore, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 483d.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb483d.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 483d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 483d_validation.pdf.gz | 396.6 KB | Display | wwPDB validaton report |
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Full document | 483d_full_validation.pdf.gz | 397.4 KB | Display | |
Data in XML | 483d_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 483d_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/83/483d ftp://data.pdbj.org/pub/pdb/validation_reports/83/483d | HTTPS FTP |
-Related structure data
Related structure data | 480dC 430dS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: RNA chain | Mass: 8744.255 Da / Num. of mol.: 1 / Fragment: 27 NA LONG SARCIN/RICIN DOMAIN / Source method: obtained synthetically Details: SEQUENCE OCCURS NATURALLY IN E.COLI 28 S RIBOSOMAL RNA |
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#2: 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: 1.97 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: 3.0 - 3.2 M (NH4)2SO4, (50 MM KMOPS, 10 MM MGCL2, 10MM MNCL2), 2.5 MG/ML RNA, pH 7.00, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
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: 14-BM-D / Wavelength: 0.9188 |
Detector | Type: ADSC / Detector: CCD / Date: May 14, 1998 / Details: BENT CYLINDRICAL SI-MIRROR |
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9188 Å / Relative weight: 1 |
Reflection | Resolution: 1.11→20 Å / Num. obs: 25407 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 35.4 |
Reflection shell | Resolution: 1.11→1.12 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.487 / % possible all: 2.3 |
Reflection | *PLUS Highest resolution: 1.11 Å / Lowest resolution: 20 Å / Observed criterion σ(I): -3 / Redundancy: 4.7 % |
Reflection shell | *PLUS % possible obs: 84.5 % / Redundancy: 2.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: THE RELATED RAT SARCIN/RICIN STRUCTURE (430D) Resolution: 1.11→20 Å / Num. parameters: 7554 / Num. restraintsaints: 10247 / Cross valid method: FREE R / σ(F): 0 Stereochemistry target values: G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, A.T. BRUNGER, H.M. BERMAN: ACTA CRYST.D, 52, 57 (1996) Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28 (1995) 53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1973) 201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 732 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.11→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5.3 % / Rfactor Rwork: 0.152 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13.5 Å2 | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.295 |