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

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Basic information

Entry
Database: PDB / ID: 1kvd
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 / SYNCHROTRON / 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 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,08411
Polymers28,4124
Non-polymers6727
Water4,035224
1
A: SMK TOXIN
B: SMK TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5906
Polymers14,2062
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-71 kcal/mol
Surface area6210 Å2
MethodPISA
2
C: SMK TOXIN
D: SMK TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4945
Polymers14,2062
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-70 kcal/mol
Surface area6070 Å2
MethodPISA
3
A: SMK TOXIN
B: SMK TOXIN
hetero molecules

A: SMK TOXIN
B: SMK TOXIN
hetero molecules

C: SMK TOXIN
D: SMK TOXIN
hetero molecules

C: SMK TOXIN
D: SMK TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,16822
Polymers56,8238
Non-polymers1,34514
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation3_654-y+3/2,x+1/2,z-1/41
crystal symmetry operation6_565x+1/2,-y+3/2,-z+1/41
Buried area24080 Å2
ΔGint-318 kcal/mol
Surface area21150 Å2
MethodPISA
4
A: SMK TOXIN
B: SMK TOXIN
hetero molecules

C: SMK TOXIN
D: SMK TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,08411
Polymers28,4124
Non-polymers6727
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x+1/2,-y+3/2,-z+1/41
Buried area11420 Å2
ΔGint-148 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.100, 81.100, 118.460
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
11C-830-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.09869, -0.87421, 0.47541), (-0.87184, -0.30628, -0.38223), (0.47975, -0.37676, -0.7924)
Vector: 86.76869, 121.78057, 23.03555)

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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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 64.1 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
21.5 Mammonium sulfate1drop
350 mMglycine-HCl1drop
48 mMcitrate-PO41drop
570 mM1dropNaCl
60.5 mMEDTA 1drop
70.05 MPMSF1drop
82.7 Mammonium sulfate1reservoir
990 mMglycine-HCl1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Mar 10, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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

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 0.008 ANGSTROMS INITIAL REFINEMENTS WERE DONE WITH X-PLOR 3.1 BY BRUNGER.
RfactorNum. reflection
Rwork0.186 -
obs-33901
Displacement parametersBiso mean: 19.11 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 35 224 2247
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.030.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3181.5
X-RAY DIFFRACTIONp_mcangle_it1.9832
X-RAY DIFFRACTIONp_scbond_it2.1982
X-RAY DIFFRACTIONp_scangle_it3.1212.5
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1770.15
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.160.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1780.3
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor15.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.720
X-RAY DIFFRACTIONp_special_tor

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