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Yorodumi- PDB-4fbs: Structure of monomeric NT from Euprosthenops australis Major Ampu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fbs | ||||||
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Title | Structure of monomeric NT from Euprosthenops australis Major Ampullate Spidroin 1 (MaSp1) | ||||||
Components | Major ampullate spidroin 1 | ||||||
Keywords | STRUCTURAL PROTEIN / 5-helix bundle / pH regulation / spider silk assembly / Extracellular | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Euprosthenops australis (spider) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Askarieh, G. / Hedhammar, M. / Rising, A. / Johansson, J. / Knight, S.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: pH-Dependent Dimerization of Spider Silk N-Terminal Domain Requires Relocation of a Wedged Tryptophan Side Chain Authors: Jaudzems, K. / Askarieh, G. / Landreh, M. / Nordling, K. / Hedhammar, M. / Jornvall, H. / Rising, A. / Knight, S.D. / Johansson, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fbs.cif.gz | 84.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fbs.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 4fbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/4fbs ftp://data.pdbj.org/pub/pdb/validation_reports/fb/4fbs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14269.831 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 24-156 / Mutation: A72R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Euprosthenops australis (spider) / Gene: MaSp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05H60 | ||
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#2: Chemical | #3: 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: 2.01 Å3/Da / Density % sol: 38.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis Tris propane pH 6.5, 0.25M NaBr, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0718 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2011 / Details: Toroidal mirror |
Radiation | Monochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0718 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40.44 Å / Num. all: 12695 / Num. obs: 12385 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.7→1.761 Å / Mean I/σ(I) obs: 5.2 / % possible all: 80.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Initial NMR model of NT A72R Resolution: 1.7→40.435 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 20.71 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→40.435 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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