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Open data
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Basic information
Entry | Database: PDB / ID: 7ulr | ||||||
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Title | recombinant kappa-bungarotoxin | ||||||
![]() | Kappa-bungarotoxin | ||||||
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Function / homology | Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / acetylcholine receptor inhibitor activity / ion channel regulator activity / Snake toxin-like superfamily / ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xu, J. / Lei, X. / Chen, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of recombinant kappa-bungarotoxin at 1.8 Angstroms resolution. Authors: Xu, J. / Lei, X. / Chen, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.8 KB | Display | ![]() |
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PDB format | ![]() | 48.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1kbaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (0.587694993783, 0.666264657981, 0.459027232098), (0.673119754988, -0.717416186923, 0.17950991668), (0.448914679787, 0.203483218636, -0.87009780485)Vector: 7. ...NCS oper: (Code: given Matrix: (0.587694993783, 0.666264657981, 0.459027232098), Vector ![]() |
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Components
#1: Protein | Mass: 7413.546 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.8 % |
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Crystal grow![]() | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 117 mg/ml in 200 mM NH4Ac, pH 7.0, 1:1 with 0.15 M DL-malic acid pH 7.0, 20% PEG 3350 at 4 degree centigrade |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.77→36.71 Å / Num. obs: 19608 / % possible obs: 93 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.047 / Rrim(I) all: 0.067 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.77→1.81 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 8.6 / Num. unique obs: 574 / CC1/2: 0.983 / Rpim(I) all: 0.092 / Rrim(I) all: 0.13 / % possible all: 86.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1KBA Resolution: 1.8→36.71 Å / SU ML: 0.1471 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 20.5678 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: 20.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→36.71 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.14223440479 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.793520574425 Å / Origin y: -3.23208132999 Å / Origin z: -10.9890284254 Å
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Refinement TLS group | Selection details: all |