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Yorodumi- PDB-4r9p: An Expansion to the Smad MH2-family: The structure of the N-MH2 e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r9p | ||||||
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Title | An Expansion to the Smad MH2-family: The structure of the N-MH2 expanded domain | ||||||
Components | RE28239p | ||||||
Keywords | TRANSCRIPTION / MH2-like domain / Beta-sandwich / Smad/FHA family | ||||||
Function / homology | Function and homology information trachea morphogenesis / apical part of cell / regulation of DNA-templated transcription / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.592 Å | ||||||
Authors | Beich-Frandsen, M. / Aragon, E. / Llimargas, M. / Benach, J. / Riera, A. / Macias, M.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structure of the N-terminal domain of the protein Expansion: an 'Expansion' to the Smad MH2 Authors: Beich-Frandsen, M. / Aragon, E. / Llimargas, M. / Benach, J. / Riera, A. / Pous, J. / Macias, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r9p.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r9p.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 4r9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/4r9p ftp://data.pdbj.org/pub/pdb/validation_reports/r9/4r9p | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27997.189 Da / Num. of mol.: 1 / Fragment: N-terminal MH2-like domain, UNP residues 1-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG13188 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta / References: UniProt: Q7YU38, UniProt: A1Z8R1*PLUS |
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#2: 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: 1.63 Å3/Da / Density % sol: 24.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 12% v/v 1,2-Propanediol, 9% w/v PEG 20000, 0.1M Glycine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97952 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2013 |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97952 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→31.27 Å / Num. all: 24247 / Num. obs: 23152 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.89 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.592→31.267 Å / SU ML: 0.2 / σ(F): 1.39 / Phase error: 23.75 / Stereochemistry target values: Engh & Huber
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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: 1.592→31.267 Å
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Refine LS restraints |
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LS refinement shell |
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