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Open data
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Basic information
Entry | Database: PDB / ID: 4a4i | ||||||
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Title | Crystal structure of the human Lin28b cold shock domain | ||||||
![]() | PROTEIN LIN-28 HOMOLOG B | ||||||
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Function / homology | ![]() negative regulation of pre-miRNA processing / positive regulation of miRNA catabolic process / negative regulation of primary miRNA processing / RNA destabilization / miRNA catabolic process / RNA 3'-end processing / pre-miRNA processing / sequence-specific double-stranded DNA binding / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mayr, F. / Schuetz, A. / Doege, N. / Heinemann, U. | ||||||
![]() | ![]() 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 "BA" 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.3 KB | Display | ![]() |
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PDB format | ![]() | 63.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 308.9 KB | Display | ![]() |
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Full document | ![]() | 310.2 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 9880.287 Da / Num. of mol.: 2 / Fragment: COLD SHOCK DOMAIN, RESIDUES 24-111 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | ![]() #3: Chemical | ChemComp-SO4 / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.3 % / Description: NONE |
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Crystal grow![]() | pH: 6.5 / Details: 2 M AMMONIUM SULFATE, 0.2 M NACL, 0.1 M MES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.95→48.59 Å / Num. obs: 16277 / % possible obs: 96.6 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.95→1.98 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.1 / % possible all: 94.4 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.592 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→48.59 Å
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Refine LS restraints |
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