+Open data
-Basic information
Entry | Database: PDB / ID: 1kvd | ||||||
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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 / SYNCHROTRON / 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 | 1kvd.cif.gz | 62.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kvd.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kvd ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kvd | HTTPS FTP |
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-Related structure data
-Links
-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: |
-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: Chemical | ChemComp-SO4 / #4: 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: 64.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
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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 % |
-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 0.008 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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