+Open data
-Basic information
Entry | Database: PDB / ID: 4a75 | ||||||
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Title | The Lin28b Cold shock domain in complex with hexathymidine. | ||||||
Components |
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Keywords | CHAPERONE/DNA / CHAPERONE-DNA COMPLEX / CHAPERONE / DNA/RNA-BINDING PROTEIN | ||||||
Function / homology | Function and homology information pre-miRNA processing / mRNA binding / nucleolus / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | XENOPUS TROPICALIS synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.75 Å | ||||||
Authors | Mayr, F. / Schuetz, A. / Doege, N. / Heinemann, U. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: The Lin28 Cold-Shock Domain Remodels Pre-Let-7 Microrna. Authors: Mayr, F. / Schutz, A. / Doge, N. / Heinemann, U. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a75.cif.gz | 169 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a75.ent.gz | 135.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a75_validation.pdf.gz | 467.6 KB | Display | wwPDB validaton report |
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Full document | 4a75_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 4a75_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 4a75_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/4a75 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/4a75 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 9942.231 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) XENOPUS (SILURANA) TROPICALIS (tropical clawed frog) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B4F6I0 #2: DNA chain | Mass: 1780.199 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.47 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 0.75 mM protein-DNA complex (in 20 mM Tris/HCl, pH 7.5, 100 mM KCl, 2 mM MgCl2 and 1 mM DTT) and 0.1 mM Bis-Tris, pH 5.5, 15% (w/v) PEG 3350 and 0.1 ...Details: 0.75 mM protein-DNA complex (in 20 mM Tris/HCl, pH 7.5, 100 mM KCl, 2 mM MgCl2 and 1 mM DTT) and 0.1 mM Bis-Tris, pH 5.5, 15% (w/v) PEG 3350 and 0.1 M sodium thiocyanate as reservoir buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: BL14-1 / Type: BESSY / Wavelength: 0.98141 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98141 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→32.91 Å / Num. obs: 39188 / % possible obs: 89.4 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.078 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.75→1.85 Å / Mean I/σ(I) obs: 3.3 / Rrim(I) all: 0.39 / % possible all: 87.8 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.75→32.91 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.836 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→32.91 Å
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