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Yorodumi- PDB-4ljm: Crystal structure of C-terminal RNA recognition motif of human ETR3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ljm | ||||||
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Title | Crystal structure of C-terminal RNA recognition motif of human ETR3 | ||||||
Components | CUGBP Elav-like family member 2 | ||||||
Keywords | RNA BINDING PROTEIN / RRM / RNA binding / RNA / CELF family | ||||||
Function / homology | Function and homology information mRNA splice site recognition / pre-mRNA binding / Flemming body / regulation of heart contraction / regulation of alternative mRNA splicing, via spliceosome / RNA processing / mRNA 3'-UTR binding / ribonucleoprotein complex / intracellular membrane-bounded organelle / RNA binding ...mRNA splice site recognition / pre-mRNA binding / Flemming body / regulation of heart contraction / regulation of alternative mRNA splicing, via spliceosome / RNA processing / mRNA 3'-UTR binding / ribonucleoprotein complex / intracellular membrane-bounded organelle / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Kashyap, M. / Sharma, A. / Yogavel, M. / Bhavesh, N.S. | ||||||
Citation | Journal: To be Published Title: Crystal structure of C-terminal RNA recognition motif of human ETR3 Authors: Kashyap, M. / Sharma, A. / Yogavel, M. / Bhavesh, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ljm.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ljm.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ljm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/4ljm ftp://data.pdbj.org/pub/pdb/validation_reports/lj/4ljm | HTTPS FTP |
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-Related structure data
Related structure data | 1b7fS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 10930.555 Da / Num. of mol.: 2 / Fragment: RRM 3 domain, UNP residues 416-508 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CELF2 / Production host: Escherichia coli (E. coli) / References: UniProt: O95319 #2: 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: 6.348 Å3/Da / Density % sol: 80.625 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.8M Ammonium citrate dibasic, 0.1M Sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 10, 2010 |
Radiation | Monochromator: VariMax Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→48.44 Å / Num. all: 11362 / Num. obs: 10792 / % possible obs: 99.71 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B7F Resolution: 3→48.44 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.925 / SU B: 17.098 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.268 / ESU R Free: 0.221 / 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: 48.641 Å2
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Refinement step | Cycle: LAST / Resolution: 3→48.44 Å
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Refine LS restraints |
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