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Yorodumi- PDB-7q8a: Crystal structure of tandem domain RRM1-2 of FUBP-interacting rep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q8a | |||||||||
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Title | Crystal structure of tandem domain RRM1-2 of FUBP-interacting repressor (FIR) bound to FUSE ssDNA fragment | |||||||||
Components |
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Keywords | TRANSCRIPTION / RNA recognition motif(RRM) / ssDNA / Structural Genomics / Structural Genomics Consortium / SGC | |||||||||
Function / homology | Function and homology information alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding / RNA binding ...alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding / RNA binding / nucleoplasm / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Ni, X. / Joerger, A.C. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC) | |||||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of tandem domain RRM1-2 of FIR bound to FUSE ssDNA fragment Authors: Ni, X. / Joerger, A.C. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q8a.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q8a.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 7q8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/7q8a ftp://data.pdbj.org/pub/pdb/validation_reports/q8/7q8a | HTTPS FTP |
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-Related structure data
Related structure data | 2qfjS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 22046.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PUF60, FIR, ROBPI, SIAHBP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UHX1 #2: DNA chain | | Mass: 588.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: DNA chain | | Mass: 563.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.29 Å3/Da / Density % sol: 46.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 25% w/v PEG3350, 0.2M Sodium acetate trihydrate, 0.1M Bis-Tris , pH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999998 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→42.5 Å / Num. obs: 26557 / % possible obs: 98.9 % / Redundancy: 4.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.05→2.11 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 1979 / CC1/2: 0.773 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QFJ Resolution: 2.05→42.5 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 25.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→42.5 Å
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Refine LS restraints |
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LS refinement shell |
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