+Open data
-Basic information
Entry | Database: PDB / ID: 3d2n | ||||||
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Title | Crystal structure of MBNL1 tandem zinc finger 1 and 2 domain | ||||||
Components | Muscleblind-like protein 1 | ||||||
Keywords | METAL BINDING / RNA BINDING PROTEIN / tandem zinc finger domain / Alternative splicing / Metal-binding / Nucleus / RNA-binding / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information regulatory region RNA binding / myoblast differentiation / embryonic limb morphogenesis / regulation of RNA splicing / RNA splicing / mRNA processing / cytoplasmic stress granule / double-stranded RNA binding / nervous system development / in utero embryonic development ...regulatory region RNA binding / myoblast differentiation / embryonic limb morphogenesis / regulation of RNA splicing / RNA splicing / mRNA processing / cytoplasmic stress granule / double-stranded RNA binding / nervous system development / in utero embryonic development / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Teplova, M. / Patel, D.J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1. Authors: Teplova, M. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d2n.cif.gz | 28 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d2n.ent.gz | 17.6 KB | Display | PDB format |
PDBx/mmJSON format | 3d2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/3d2n ftp://data.pdbj.org/pub/pdb/validation_reports/d2/3d2n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9621.984 Da / Num. of mol.: 1 Fragment: tandem zinc finger 1 and 2 domains (UNP residues 9-90) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MBNL1, EXP, KIAA0428, MBNL / Plasmid: Pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9NR56 | ||
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#2: Chemical | #3: 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: 2.63 Å3/Da / Density % sol: 53.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.2 Details: 20% PEG 4000, 0.1M sodium citrate, 20 % isopropanol, pH 7.2, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2821 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2821 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 5336 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rsym value: 0.06 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.274 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.877 / SU B: 33.586 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R: 1.749 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 50.872 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.702→2.771 Å / Total num. of bins used: 20
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