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- PDB-4gvb: Crystal structure of the virally encoded antifungal protein, KP6,... -

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Basic information

Entry
Database: PDB / ID: 4gvb
TitleCrystal structure of the virally encoded antifungal protein, KP6, heterodimer
Components
  • KP6 killer toxin subunit alpha
  • KP6 killer toxin subunit beta
KeywordsTOXIN / Antifungal protein / Secreted
Function / homologyKiller toxin KP6 alpha-subunit / toxin activity / Alpha-Beta Plaits / 2-Layer Sandwich / extracellular region / Alpha Beta / KP6 killer toxin
Function and homology information
Biological speciesUstilago maydis virus P6
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSmith, T.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: The Atomic Structure of the Virally Encoded Antifungal Protein, KP6.
Authors: Allen, A. / Chatt, E. / Smith, T.J.
History
DepositionAug 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 13, 2013Group: Database references
Revision 1.3Nov 20, 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

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Assembly

Deposited unit
A: KP6 killer toxin subunit alpha
B: KP6 killer toxin subunit beta


Theoretical massNumber of molelcules
Total (without water)18,0362
Polymers18,0362
Non-polymers00
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-5 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.419, 44.419, 155.648
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-101-

HOH

21B-131-

HOH

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Components

#1: Protein KP6 killer toxin subunit alpha / VP10


Mass: 8893.862 Da / Num. of mol.: 1 / Fragment: KP6 alpha subunit / Source method: isolated from a natural source / Source: (natural) Ustilago maydis virus P6 / References: UniProt: P16948
#2: Protein KP6 killer toxin subunit beta / VP12.5


Mass: 9142.168 Da / Num. of mol.: 1 / Fragment: KP6 beta subunit / Source method: isolated from a natural source / Source: (natural) Ustilago maydis virus P6 / References: UniProt: P16948
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Reservoir solution contained 50 mM Tris, pH 8.0, 0.7 M ammonium sulfate, and 1 mM sodium azide. The drops were composed of 1:1 ratio of reservoir solution and 8.2 mg/ml KP6, VAPOR DIFFUSION, ...Details: Reservoir solution contained 50 mM Tris, pH 8.0, 0.7 M ammonium sulfate, and 1 mM sodium azide. The drops were composed of 1:1 ratio of reservoir solution and 8.2 mg/ml KP6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 12, 2012 / Details: mirrors
RadiationMonochromator: Osmic (blue) mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→39 Å / Num. all: 13869 / Num. obs: 13869 / % possible obs: 93.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.2 %
Reflection shellResolution: 1.8→1.89 Å / % possible all: 90.5

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.1_353)refinement
SAINTdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.468 Å / SU ML: 0.23 / σ(F): 0.08 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 753 4.99 %Random
Rwork0.2148 ---
obs0.2164 -86.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.721 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7075 Å20 Å2-0 Å2
2--3.7075 Å20 Å2
3----7.4151 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 0 168 1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071209
X-RAY DIFFRACTIONf_angle_d0.9651623
X-RAY DIFFRACTIONf_dihedral_angle_d12.476417
X-RAY DIFFRACTIONf_chiral_restr0.075162
X-RAY DIFFRACTIONf_plane_restr0.004214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.9390.32371280.28972359X-RAY DIFFRACTION73
1.939-2.13410.29431340.25192560X-RAY DIFFRACTION79
2.1341-2.44290.31281550.23442754X-RAY DIFFRACTION85
2.4429-3.07760.24831710.21573187X-RAY DIFFRACTION97
3.0776-38.47680.20691650.19363465X-RAY DIFFRACTION99

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