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Yorodumi- PDB-1di2: CRYSTAL STRUCTURE OF A DSRNA-BINDING DOMAIN COMPLEXED WITH DSRNA:... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1di2 | ||||||
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Title | CRYSTAL STRUCTURE OF A DSRNA-BINDING DOMAIN COMPLEXED WITH DSRNA: MOLECULAR BASIS OF DOUBLE-STRANDED RNA-PROTEIN INTERACTIONS | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / PROTEIN-RNA COMPLEX / DOUBLE STRANDED RNA / PROTEIN-RNA INTERACTIONS / RNA-BINING PROTEIN / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information siRNA processing / enzyme activator activity / double-stranded RNA binding / nucleolus / perinuclear region of cytoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SIR / Resolution: 1.9 Å | ||||||
Authors | Ryter, J.M. / Schultz, S.C. | ||||||
Citation | Journal: EMBO J. / Year: 1998 Title: Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA. Authors: Ryter, J.M. / Schultz, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1di2.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1di2.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 1di2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1di2_validation.pdf.gz | 480.8 KB | Display | wwPDB validaton report |
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Full document | 1di2_full_validation.pdf.gz | 485.3 KB | Display | |
Data in XML | 1di2_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1di2_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/1di2 ftp://data.pdbj.org/pub/pdb/validation_reports/di/1di2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 3206.981 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: T7 TRANSCRIPTION OF SYNTHETIC DNA OLIGONUCLEOTIDES #2: Protein | Mass: 7689.862 Da / Num. of mol.: 2 / Fragment: SECOND DSRNA BINDING DOMAIN / Mutation: N112M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91836 #3: 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: 3.6 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: PEG 4000, ETHYLENE GLYCOL, KCL, NACL, MES, DTT, BETA-MERCAPTOETHANOL, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 25, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→99 Å / Num. all: 28729 / Num. obs: 26083 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 1.66 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.5 / % possible all: 50 |
Reflection shell | *PLUS % possible obs: 50 % |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 1.9→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 346673.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 Stereochemistry target values: ENGH & HUBER AND PARKINSON ET AL.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.79 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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