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- PDB-1kpt: STRUCTURE AND FUNCTION OF A VIRALLY ENCODED FUNGAL TOXIN FROM UST... -

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Basic information

Entry
Database: PDB / ID: 1kpt
TitleSTRUCTURE AND FUNCTION OF A VIRALLY ENCODED FUNGAL TOXIN FROM USTILAGO MAYDIS: A FUNGAL AND MAMMALIAN CALCIUM CHANNEL INHIBITOR
ComponentsKP4 TOXIN
KeywordsTOXIN / KILLER TOXIN / VIRALLY ENCODED / SINGLE SUBUNIT / ALPHA/BETA FAMILY / LEFT-HANDED CROSSOVER / USTILAGO MAYDIS / FUNGAL TOXIN
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Killer Toxin P4, subunit A / Killer toxin, Kp4 / Kp4 / Killer Toxin P4; Chain A / Killer toxin Kp4/SMK / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesUstilago maydis (corn smut)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsGu, F. / Smith, T.
Citation
Journal: Structure / Year: 1995
Title: Structure and function of a virally encoded fungal toxin from Ustilago maydis: a fungal and mammalian Ca2+ channel inhibitor.
Authors: Gu, F. / Khimani, A. / Rane, S.G. / Flurkey, W.H. / Bozarth, R.F. / Smith, T.J.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: The Characterization and Crystallization of a Virally Encoded Ustilago Maydis Kp4 Toxin
Authors: Gu, F. / Sullivan, T. / Che, Z. / Ganesa, C. / Flurkey, W. / Bozarth, R. / Smith, T.
History
DepositionJun 6, 1995Processing site: BNL
Revision 1.0Oct 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KP4 TOXIN
B: KP4 TOXIN


Theoretical massNumber of molelcules
Total (without water)22,1352
Polymers22,1352
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.140, 63.760, 53.620
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.0067, 0.0043), (0.0067, 0.4191, 0.9079), (0.0043, 0.9079, -0.4191)
Vector: 64.0134, -16.4806, 25.2845)

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Components

#1: Protein KP4 TOXIN / P4 TOXIN / KP4 KILLER TOXIN


Mass: 11067.370 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SECRETED / Source: (natural) Ustilago maydis (corn smut) / Strain: P4 STRAIN OF USTILAGO MAYDIS SUBSTRAIN M2B / References: UniProt: Q90121
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Msodium citrate1reservoir
220 %isopropanol1reservoir
30.1 MHEPES1reservoir
410 mg/mlKP4 toxin1drop
50.2 Msodium citrate1drop
620 %isopropanol1drop
70.1 MHEPES1drop

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 21, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 15905 / % possible obs: 88.7 % / Observed criterion σ(I): 3 / Redundancy: 3 % / Rmerge(I) obs: 0.052
Reflection
*PLUS
% possible obs: 81.9 % / Redundancy: 3.42 % / Rmerge(I) obs: 0.052

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.75→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.216 -5 %
Rwork0.174 --
obs0.174 14697 84.7 %
Displacement parametersBiso mean: 16.82 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.75→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 0 140 1733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.323
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Rfactor obs: 0.186 / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0189
X-RAY DIFFRACTIONx_angle_deg1.95

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