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- PDB-6x1i: Two-Component D3 Assembly Constructed by Fusing Symmetric Oligome... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6x1i | ||||||
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Title | Two-Component D3 Assembly Constructed by Fusing Symmetric Oligomers to Coiled Coils | ||||||
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![]() | BIOSYNTHETIC PROTEIN / Two-Component / Self-Assembling / Symmetric / D3 / Coiled Coil / Helical Fusion / Design | ||||||
Function / homology | ![]() corrinoid adenosyltransferase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Laniado, J. / Yeates, T.O. / Sawaya, M.R. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.8 KB | Display | ![]() |
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PDB format | ![]() | 114 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409.8 KB | Display | ![]() |
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Full document | ![]() | 413.3 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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.) ![]() ![]() ![]() ![]() Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH0671 / Production host: ![]() ![]() |
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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.) ![]() ![]() Strain: C58 / ATCC 33970 / Gene: Atu0744 / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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 |