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Yorodumi- PDB-5fgp: Crystal structure of D. melanogaster Pur-alpha repeat I-II in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fgp | |||||||||
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Title | Crystal structure of D. melanogaster Pur-alpha repeat I-II in complex with DNA. | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA-protein interaction / RNA-protein interaction / DNA unwinding / FXTAS / ALS / FTLD / 5q31.3 microdeletion syndrome / neurodegeneration | |||||||||
Function / homology | Function and homology information purine-rich negative regulatory element binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / mRNA binding / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Weber, J. / Janowski, R. / Niessing, D. | |||||||||
Citation | Journal: Elife / Year: 2016 Title: Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha. Authors: Weber, J. / Bao, H. / Hartlmuller, C. / Wang, Z. / Windhager, A. / Janowski, R. / Madl, T. / Jin, P. / Niessing, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fgp.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fgp.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fgp_validation.pdf.gz | 444.5 KB | Display | wwPDB validaton report |
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Full document | 5fgp_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 5fgp_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 5fgp_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/5fgp ftp://data.pdbj.org/pub/pdb/validation_reports/fg/5fgp | HTTPS FTP |
-Related structure data
Related structure data | 5fgoC 3k44S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17495.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Pur-alpha, CG1507, Dmel_CG1507 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V4D9, UniProt: Q95RR6*PLUS |
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#2: DNA chain | Mass: 2179.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.87 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 50 mM MES pH 5.2, 500 mM (NH4)2SO4, 1 mM TCEP and 16 % PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 11349 / % possible obs: 99.4 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 18.85 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.61 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K44 Resolution: 2→41.934 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→41.934 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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