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- PDB-1kve: KILLER TOXIN FROM HALOTOLERANT YEAST -

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Basic information

Entry
Database: PDB / ID: 1kve
TitleKILLER TOXIN FROM HALOTOLERANT YEAST
Components(SMK TOXIN) x 2
KeywordsTOXIN / 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
Smk Toxin, Beta chain / Smk Toxin, beta chain / Smk Toxin, alpha chain / Smk Toxin, alpha chain / Killer toxin, SMK, beta subunit / Salt-mediated killer toxin, alpha subunit / Killer toxin SMK, beta subunit superfamily / : / Salt-mediated killer protoxin 1, beta subunit / SMK1 alpha subunit ...Smk Toxin, Beta chain / Smk Toxin, beta chain / Smk Toxin, alpha chain / Smk Toxin, alpha chain / Killer toxin, SMK, beta subunit / Salt-mediated killer toxin, alpha subunit / Killer toxin SMK, beta subunit superfamily / : / Salt-mediated killer protoxin 1, beta subunit / SMK1 alpha subunit / Killer toxin Kp4/SMK / Few Secondary Structures / Irregular / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Salt-mediated killer protoxin 1
Similarity search - Component
Biological speciesPichia farinosa (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsKashiwagi, 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
DepositionOct 4, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMK TOXIN
B: SMK TOXIN
C: SMK TOXIN
D: SMK TOXIN


Theoretical massNumber of molelcules
Total (without water)28,4124
Polymers28,4124
Non-polymers00
Water4,882271
1
A: SMK TOXIN
B: SMK TOXIN


Theoretical massNumber of molelcules
Total (without water)14,2062
Polymers14,2062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-34 kcal/mol
Surface area6010 Å2
MethodPISA
2
C: SMK TOXIN
D: SMK TOXIN


Theoretical massNumber of molelcules
Total (without water)14,2062
Polymers14,2062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-31 kcal/mol
Surface area5900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.120, 81.120, 118.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-567-

HOH

21B-592-

HOH

31C-830-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.09656, -0.87326, 0.47759), (-0.87074, -0.30656, -0.38449), (0.48217, -0.37873, -0.78998)
Vector: 86.70187, 121.76711, 23.09693)

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Components

#1: Protein SMK TOXIN


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 SMK TOXIN


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 / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.2 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
215 %(w/v)PEG40001drop
3100 mMammonium sulfate1drop
4100 mMglycine-HCl1drop
58 mMcitrate-PO41drop
670 mM1dropNaCl
70.5 mMEDTA1drop
80.05 MPMSF1drop
925 %(w/v)PEG40001reservoir
10167 mMammonium sulfate1reservoir
11167 mMglycine-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 20, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1model building
PROLSQrefinement
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 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.
RfactorNum. reflection
Rwork0.172 -
obs-34347
Displacement parametersBiso mean: 22.49 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 0 271 2259
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0270.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1281.5
X-RAY DIFFRACTIONp_mcangle_it1.7922
X-RAY DIFFRACTIONp_scbond_it1.9972
X-RAY DIFFRACTIONp_scangle_it2.9352.5
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1660.15
X-RAY DIFFRACTIONp_singtor_nbd0.1670.3
X-RAY DIFFRACTIONp_multtor_nbd0.1470.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1640.3
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor14.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS

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