+Open data
-Basic information
Entry | Database: PDB / ID: 1kve | ||||||
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Title | KILLER TOXIN FROM HALOTOLERANT YEAST | ||||||
Components | (SMK TOXIN) x 2 | ||||||
Keywords | TOXIN / HALOTOLERANT YEAST | ||||||
Function / homology | Function and homology information toxin sequestering activity / toxin activity / killing of cells of another organism / protein-containing complex / extracellular region Similarity search - Function | ||||||
Biological species | Pichia farinosa (fungus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Kashiwagi, T. / Kunishima, N. / Suzuki, C. / Tsuchiya, F. / Nikkuni, S. / Arata, Y. / Morikawa, K. | ||||||
Citation | Journal: Structure / Year: 1997 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: Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kve.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kve.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 1kve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kve_validation.pdf.gz | 431.2 KB | Display | wwPDB validaton report |
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Full document | 1kve_full_validation.pdf.gz | 431.7 KB | Display | |
Data in XML | 1kve_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 1kve_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kve ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kve | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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: (0.09656, -0.87326, 0.47759), Vector: |
-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) Pichia farinosa (fungus) / Strain: KK1 / References: UniProt: P19972 #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) Pichia farinosa (fungus) / Strain: KK1 / References: UniProt: P19972 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4 Details: CRYSTALS WERE GROWN FROM 25% POLYETHYLENE GLYCOL SOLUTION AT PH 4.0. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 20, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 35468 / % possible obs: 94.7 % / Observed criterion σ(I): 0.5 / Redundancy: 5.23 % / Rmerge(I) obs: 0.062 |
Reflection | *PLUS Num. measured all: 185448 |
-Processing
Software |
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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 0.007 ANGSTROMS INITIAL REFINEMENTS WERE DONE WITH X-PLOR 3.1 BY BRUNGER.
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Displacement parameters | Biso mean: 22.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.172 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |