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- PDB-2bhi: Crystal structure of Taiwan cobra cardiotoxin A3 complexed with s... -

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Basic information

Entry
Database: PDB / ID: 2bhi
TitleCrystal structure of Taiwan cobra cardiotoxin A3 complexed with sulfogalactoceramide
ComponentsCYTOTOXIN 3
KeywordsCARDIOTOXIN / COBRA CARDIOTOXIN / SULFOGALACTOCERAMIDE SULFATIDE / GLYCOSPHINGOLIPID / MEMBRANE PORE FORMATION / CYTOLYSIS
Function / homology
Function and homology information


cytolysis / other organism cell membrane / toxin activity / killing of cells of another organism / extracellular region / membrane
Similarity search - Function
Snake cytotoxin, cobra-type / Snake three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
HEXAETHYLENE GLYCOL MONODECYL ETHER / SULFOGALACTOCERAMIDE / Cytotoxin 4 / Cytotoxin 3
Similarity search - Component
Biological speciesNAJA ATRA (Chinese cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsWang, C.-H. / Liu, J.-H. / Wu, P.-L. / Lee, S.-C. / Hsiao, C.-D. / Wu, W.-G.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Glycosphingolipid-Facilitated Membrane Insertion and Internalization of Cobra Cardiotoxin: The Sulfatide/Cardiotoxin Complex Structure in a Membrane-Like Environment Suggests a Lipid-Dependent ...Title: Glycosphingolipid-Facilitated Membrane Insertion and Internalization of Cobra Cardiotoxin: The Sulfatide/Cardiotoxin Complex Structure in a Membrane-Like Environment Suggests a Lipid-Dependent Cell-Penetrating Mechanism for Membrane Binding Polypeptides.
Authors: Wang, C.-H. / Liu, J.-H. / Lee, S.-C. / Hsiao, C.-D. / Wu, W.-G.
History
DepositionJan 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOTOXIN 3
B: CYTOTOXIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,07414
Polymers13,5172
Non-polymers5,55712
Water1,802100
1
A: CYTOTOXIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2028
Polymers6,7581
Non-polymers3,4447
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOTOXIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8716
Polymers6,7581
Non-polymers2,1135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.327, 63.327, 120.879
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

21A-2013-

HOH

31A-2032-

HOH

41B-2003-

HOH

51B-2011-

HOH

61B-2051-

HOH

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Components

#1: Protein CYTOTOXIN 3 / CARDIOTOXIN 3 / CTX-3 / CARDIOTOXIN ANALOG III / CTX IIICARDIOTOXIN 3


Mass: 6758.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) NAJA ATRA (Chinese cobra) / Organ: VENOM GLAND / References: UniProt: P01444, UniProt: P60301*PLUS
#2: Chemical ChemComp-SFT / SULFOGALACTOCERAMIDE / SULFATIDE


Mass: 908.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H93NO12S
#3: Chemical
ChemComp-C10 / HEXAETHYLENE GLYCOL MONODECYL ETHER


Mass: 422.596 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C22H46O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBELONGS TO THE SNAKE TOXIN FAMILY.

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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: 2.6 Å3/Da / Density % sol: 52.2 %
Crystal growpH: 7
Details: 1.8 M SODIUM MALONATE, 7.5% (V/V) TERT-BUTANOL, 7.5% (V/V) PENTAERYTHRITOL ETHOXYLATE (15/4 EO/OH), 0.08% (W/V) C10E6, 50 MM IMIDAZOLE, AND 50 MM TRIS-HCL, PH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.1271
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 18, 2004 / Details: MIRRORS
RadiationMonochromator: DCM WITH SAGITTAL FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.3→26.5 Å / Num. obs: 6821 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H0J

1h0j


Resolution: 2.31→26.47 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 521475.44 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.222 501 8.2 %RANDOM
Rwork0.219 ---
obs0.219 6126 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.1255 Å2 / ksol: 0.370974 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å23.08 Å20 Å2
2--2.31 Å20 Å2
3----4.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.31→26.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 246 100 1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.44
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.272.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.202 67 8.4 %
Rwork0.206 731 -
obs--72.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5LIGAND.PARLIGAND.TOP

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