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Yorodumi- PDB-4ndl: Computational design and experimental verification of a symmetric... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ndl | ||||||
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Title | Computational design and experimental verification of a symmetric homodimer | ||||||
Components | ENH-c2b, computational designed homodimer | ||||||
Keywords | DE NOVO PROTEIN / helix-turn-helix | ||||||
Function / homology | Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha Function and homology information | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Mou, Y. / Huang, P.S. / Hsu, F.C. / Huang, S.J. / Mayo, S.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Computational design and experimental verification of a symmetric protein homodimer. Authors: Mou, Y. / Huang, P.S. / Hsu, F.C. / Huang, S.J. / Mayo, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ndl.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ndl.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ndl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/4ndl ftp://data.pdbj.org/pub/pdb/validation_reports/nd/4ndl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 8848.906 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) #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: 2.06 Å3/Da / Density % sol: 40.2 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 1% w/v tryptone, 20% w/v polyethylene glycerol 3350, 0.05 M HEPES sodium, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.915 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 24, 2011 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.915 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→24.6 Å / Num. obs: 5697 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→24.6 Å / SU ML: 0.46 / σ(F): 1.53 / Phase error: 31.58 / 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: 3.5→24.6 Å
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Refine LS restraints |
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