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Yorodumi- PDB-6x1i: Two-Component D3 Assembly Constructed by Fusing Symmetric Oligome... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x1i | ||||||
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Title | Two-Component D3 Assembly Constructed by Fusing Symmetric Oligomers to Coiled Coils | ||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / Two-Component / Self-Assembling / Symmetric / D3 / Coiled Coil / Helical Fusion / Design | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) Pyrococcus horikoshii OT3 (archaea) Agrobacterium fabrum str. C58 (bacteria) Agrobacterium fabrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.32 Å | ||||||
Authors | Laniado, J. / Yeates, T.O. / Sawaya, M.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Nano / Year: 2021 Title: Geometric Lessons and Design Strategies for Nanoscale Protein Cages. Authors: Laniado, J. / Cannon, K.A. / Miller, J.E. / Sawaya, M.R. / McNamara, D.E. / Yeates, T.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x1i.cif.gz | 159.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x1i.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 6x1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/6x1i ftp://data.pdbj.org/pub/pdb/validation_reports/x1/6x1i | 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: 19430.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea), (gene. exp.) Pyrococcus horikoshii OT3 (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH0671 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O58404 |
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#2: Protein | Mass: 17644.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria), (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Strain: C58 / ATCC 33970 / Gene: Atu0744 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7D0S4 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.08 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: Reagent Well: - 10ul of Silver Bullets additive screen reagent B9: 0.25% w/v Hexamminecobalt(III) chloride, 0.25% w/v Salicylamide, 0.25% w/v Sulfanilamide, 0.25% w/v Vanillic acid, 0.02 M ...Details: Reagent Well: - 10ul of Silver Bullets additive screen reagent B9: 0.25% w/v Hexamminecobalt(III) chloride, 0.25% w/v Salicylamide, 0.25% w/v Sulfanilamide, 0.25% w/v Vanillic acid, 0.02 M HEPES sodium pH 6.8 - 90ul of crystallization reagent: 0.10 M Sodium Acetate pH 5.4, 66% MPD Drop: - 2:1 protein sample to well reagent ratio - Protein sample: 2.8mg/ml of purified protein in 0.5M NaCl, 5% Glycerol, 2.8mM beta-mercaptoethanol, 50 mM Tris pH 7.5, 5mM MgCl2 sample buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 6, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.32→84.5 Å / Num. obs: 3945 / % possible obs: 99.7 % / Redundancy: 17.657 % / Biso Wilson estimate: 237.211 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.099 / Χ2: 0.998 / Net I/σ(I): 14.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WY1, 3DXO Resolution: 4.32→84.49 Å / SU ML: 0.6069 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 43.638 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 267.69 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.32→84.49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -21.6837214664 Å / Origin y: -3.49920025763 Å / Origin z: 4.27013204244 Å
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Refinement TLS group | Selection details: all |