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- PDB-1kp6: USTILAGO MAYDIS KILLER TOXIN KP6 ALPHA-SUBUNIT -

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Basic information

Entry
Database: PDB / ID: 1kp6
TitleUSTILAGO MAYDIS KILLER TOXIN KP6 ALPHA-SUBUNIT
ComponentsPROTEIN (TOXIN)
KeywordsTOXIN / KILLER TOXIN / ION CHANNEL MODULATOR
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 (corn smut)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsLi, N. / Erman, M. / Pangborn, W. / Duax, W.L. / Park, C.-M. / Bruenn, J. / Ghosh, D.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Structure of Ustilago maydis killer toxin KP6 alpha-subunit. A multimeric assembly with a central pore.
Authors: Li, N. / Erman, M. / Pangborn, W. / Duax, W.L. / Park, C.M. / Bruenn, J. / Ghosh, D.
History
DepositionMay 28, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 21, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (TOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8332
Polymers8,7371
Non-polymers961
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.300, 48.300, 124.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein PROTEIN (TOXIN)


Mass: 8736.669 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ustilago maydis (corn smut) / References: UniProt: P16948
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.41 Å3/Da / Density % sol: 42 %
Crystal growpH: 6 / Details: 18-21% AM. SULFATE 10MM MES PH 6.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: drop1-0.005 ml, drop2-0.001 ml
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop1
285 %ammonium sulfate1drop2
310 mMMES1drop2
418-21 %ammonium sulfate1reservoir
510 mMMES1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→99 Å / Num. obs: 8260 / % possible obs: 93.9 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.077
Reflection shellResolution: 1.8→1.85 Å / Mean I/σ(I) obs: 2.15 / % possible all: 90
Reflection
*PLUS
Num. measured all: 109467
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MIR / Resolution: 1.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.211 -10 %RANDOM
Rwork0.164 ---
obs0.164 6838 96 %-
Displacement parametersBiso mean: 17.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms761 0 5 231 997
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.309
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
Xplor fileSerial no: 1 / Param file: PARCSDX.PRO / Topol file: TOPHCSDX.PRO

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