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- PDB-1h0j: Structural Basis of the Membrane-induced Cardiotoxin A3 Oligomeri... -

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Basic information

Entry
Database: PDB / ID: 1h0j
TitleStructural Basis of the Membrane-induced Cardiotoxin A3 Oligomerization
ComponentsCARDIOTOXIN-3
KeywordsCARDIOTOXIN / SODIUM DODECYL SULFATE / VENOM / CYTOTOXIN
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 toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Cytotoxin 4 / Cytotoxin 3
Similarity search - Component
Biological speciesNAJA ATRA (Chinese cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsForouhar, F. / Huang, W.-N. / Liu, J.-H. / Chien, K.-Y. / Wu, W.-G. / Hsiao, C.-D.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structural Basis of Membrane-Induced Cardiotoxin A3 Oligomerization
Authors: Forouhar, F. / Huang, W.-N. / Liu, J.-H. / Chien, K.-Y. / Wu, W.-G. / Hsiao, C.-D.
History
DepositionJun 20, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2003Provider: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARDIOTOXIN-3
B: CARDIOTOXIN-3
C: CARDIOTOXIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,93913
Polymers20,2753
Non-polymers2,66410
Water4,630257
1
A: CARDIOTOXIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5584
Polymers6,7581
Non-polymers7993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CARDIOTOXIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0906
Polymers6,7581
Non-polymers1,3325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CARDIOTOXIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2913
Polymers6,7581
Non-polymers5332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.902, 76.202, 47.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CARDIOTOXIN-3 / CARDIOTOXIN ANALOG III / CTX III / CARDIOTOXIN C-10 CYTOTOXIN IV / CTX-3


Mass: 6758.330 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: SODIUM DODECYL SULFATE / Source: (natural) NAJA ATRA (Chinese cobra) / Organ: VENOM GLAND / References: UniProt: P01444, UniProt: P60301*PLUS
#2: Chemical
ChemComp-SDS / DODECYL SULFATE


Mass: 266.397 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C12H26O4S / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBELONGS TO THE SNAKE TOXIN FAMILY.
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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growpH: 4.6
Details: 10 MG/ML PROTEIN MIXED WITH 0.1M SODIUM ACETATE (PH 4.6), 20% PEG 400, 3% GLYCEROL, AND 24 MM SDS.
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
2100 mMsodium acetate1reservoirpH4.6
320 %PEG4001reservoir
43 %glycerol1reservoir
524 mMSDS1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 15, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 21036 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 4.47 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 28.5
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 3.91 / % possible all: 96.3
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. measured all: 93866 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 96.3 % / Rmerge(I) obs: 0.266

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TGX

1tgx


Resolution: 1.9→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 595624.89 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1847 9.8 %RANDOM
Rwork0.227 ---
obs0.227 18900 85 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 96.6429 Å2 / ksol: 0.389881 e/Å3
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å20 Å2
2--2.02 Å20 Å2
3----4.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 170 257 1822
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.28
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 255 9.9 %
Rwork0.22 2312 -
obs--70.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SDS.PARSDS.TOP
Refinement
*PLUS
Rfactor Rfree: 0.2775 / Rfactor Rwork: 0.2201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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