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Open data
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Basic information
Entry | Database: PDB / ID: 1kvd | ||||||
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Title | KILLER TOXIN FROM HALOTOLERANT YEAST | ||||||
![]() | (SMK TOXIN) x 2 | ||||||
![]() | TOXIN / HALOTOLERANT YEAST | ||||||
Function / homology | ![]() toxin sequestering activity / toxin activity / killing of cells of another organism / protein-containing complex / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kashiwagi, T. / Kunishima, N. / Suzuki, C. / Tsuchiya, F. / Nikkuni, S. / Arata, Y. / Morikawa, K. | ||||||
![]() | ![]() Title: The novel acidophilic structure of the killer toxin from halotolerant yeast demonstrates remarkable folding similarity with a fungal killer toxin. Authors: Kashiwagi, T. / Kunishima, N. / Suzuki, C. / Tsuchiya, F. / Nikkuni, S. / Arata, Y. / Morikawa, K. #1: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Studies of a Novel Killer Toxin from a Halotolerant Yeast Pichia Farinosa Authors: Kunishima, N. / Kashiwagi, T. / Suzuki, C. / Nikkuni, S. / Tsuchiya, F. / Arata, Y. / Morikawa, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.9 KB | Display | ![]() |
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PDB format | ![]() | 51.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.9 KB | Display | ![]() |
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Full document | ![]() | 442.9 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 21 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.09869, -0.87421, 0.47541), Vector: |
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Components
#1: Protein | Mass: 6349.229 Da / Num. of mol.: 2 Fragment: CHAIN A AND C ARE RESIDUES 19 - 81 OF THE ALPHA CHAIN, CHAIN B AND D ARE RESIDUES 146 - 222 OF THE BETA CHAIN Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 7856.556 Da / Num. of mol.: 2 Fragment: CHAIN A AND C ARE RESIDUES 19 - 81 OF THE ALPHA CHAIN, CHAIN B AND D ARE RESIDUES 146 - 222 OF THE BETA CHAIN Source method: isolated from a natural source / Source: (natural) ![]() #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 3.5 Details: CRYSTALS WERE GROWN FROM 2.7M AMMONIUM SULFATE SOLUTION AT PH 3.5. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Mar 10, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 35030 / % possible obs: 93.7 % / Observed criterion σ(I): 0.5 / Redundancy: 7.14 % / Rmerge(I) obs: 0.069 |
Reflection | *PLUS Num. measured all: 168550 |
Reflection shell | *PLUS % possible obs: 82.7 % |
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Processing
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Refinement | Resolution: 1.8→6 Å / σ(F): 1 Details: IDEAL BOND LENGTHS AND ANGLES USED DURING REFINEMENT HENDRICKSON AND KONNERT FINAL RMS COORD. SHIFT 0.008 ANGSTROMS INITIAL REFINEMENTS WERE DONE WITH X-PLOR 3.1 BY BRUNGER.
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Displacement parameters | Biso mean: 19.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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