+Open data
-Basic information
Entry | Database: PDB / ID: 3ulj | ||||||
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Title | Crystal structure of apo Lin28B cold shock domain | ||||||
Components | Lin28b, DNA-binding protein | ||||||
Keywords | DNA BINDING PROTEIN / beta barrel / cold shock domain fold / nucleic acid binding | ||||||
Function / homology | Function and homology information pre-miRNA processing / mRNA binding / nucleolus / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Xenopus tropicalis | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ulj.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ulj.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 3ulj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ulj_validation.pdf.gz | 452.8 KB | Display | wwPDB validaton report |
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Full document | 3ulj_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 3ulj_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 3ulj_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/3ulj ftp://data.pdbj.org/pub/pdb/validation_reports/ul/3ulj | HTTPS FTP |
-Related structure data
Related structure data | 4a4iC 4a75C 4a76C 4alpC 312zS 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 9942.231 Da / Num. of mol.: 2 / Fragment: unp residues 27-114 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus (Silurana) tropicalis (tropical clawed frog) Gene: lin28b / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: B4F6I0 #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-GOL / | #4: 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: 2.76 Å3/Da / Density % sol: 55.29 % |
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Crystal grow | Method: evaporation / pH: 7 Details: 2.5 M sodium acetate, 0.1 M HEPES , pH 7.0, EVAPORATION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98141 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98141 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→32.3 Å / Num. all: 100674 / Num. obs: 100170 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.06→1.087 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.61 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 312Z Resolution: 1.06→32.3 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / Occupancy max: 1 / Occupancy min: 0.12 / SU B: 0.56 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 66.98 Å2 / Biso mean: 15.9469 Å2 / Biso min: 3.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.06→32.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.06→1.087 Å / Total num. of bins used: 20
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