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- PDB-4tso: Crystal structure of FraC with DHPC bound (crystal form I) -

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Basic information

Entry
Database: PDB / ID: 4tso
TitleCrystal structure of FraC with DHPC bound (crystal form I)
ComponentsFragaceatoxin C
KeywordsTOXIN / actinoporin / pore-forming toxin / Membrane lipids / Phosphocholine / Lipid-protein interaction
Function / homology
Function and homology information


nematocyst / pore complex assembly / cytolysis in another organism / other organism cell membrane / pore complex / monoatomic cation transport / channel activity / toxin activity / lipid binding / extracellular region / identical protein binding
Similarity search - Function
Sea anemone actinoporin-like / : / Sea anemone cytotoxic protein / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,2-dihexanoyl-sn-glycero-3-phosphocholine / PHOSPHATE ION / DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesActinia fragacea (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCaaveiro, J.M.M. / Tanaka, K. / Tsumoto, K.
Citation
Journal: Nat Commun / Year: 2015
Title: Structural basis for self-assembly of a cytolytic pore lined by protein and lipid
Authors: Tanaka, K. / Caaveiro, J.M.M. / Morante, K. / Gonzalez-Manas, J.M. / Tsumoto, K.
#1: Journal: Toxicon / Year: 2009
Title: Purification, cloning and characterization of fragaceatoxin C, a novel actinoporin from the sea anemone Actinia fragacea
Authors: Bellomio, A. / Morante, K. / Barlic, A. / Gutierrez-Aguirre, I. / Viguera, A.R. / Gonzalez-Manas, J.M.
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fragaceatoxin C
B: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,62316
Polymers39,4932
Non-polymers3,13114
Water2,090116
1
A: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4918
Polymers19,7461
Non-polymers1,7457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1328
Polymers19,7461
Non-polymers1,3867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.059, 131.059, 49.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-206-

PO4

21B-206-

PO4

31B-207-

PO4

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Components

#1: Protein Fragaceatoxin C / fraC


Mass: 19746.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinia fragacea (sea anemone) / Plasmid: pGEM-T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9W5G6
#2: Chemical
ChemComp-HXG / 1,2-dihexanoyl-sn-glycero-3-phosphocholine / (4R,7R)-7-(hexanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphapentadecan-1-aminium 4-oxide


Mass: 454.515 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H41NO8P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 50 mM DHPC, 200 mM Li2SO4, 20% PEG 1000, 100 mM phosphate-citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→32.76 Å / Num. obs: 21326 / % possible obs: 97.5 % / Redundancy: 8.4 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 18.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.3 / % possible all: 95.7

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VWI

3vwi


Resolution: 2.3→32.76 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.04 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22687 1106 5.2 %RANDOM
Rwork0.18233 ---
obs0.18455 20217 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.992 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.69 Å20 Å2
2---0.69 Å20 Å2
3---2.24 Å2
Refinement stepCycle: 1 / Resolution: 2.3→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 195 116 3079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023037
X-RAY DIFFRACTIONr_bond_other_d0.0070.0212886
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9834107
X-RAY DIFFRACTIONr_angle_other_deg1.3063.0236597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7955356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07422.576132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53215458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0071522
X-RAY DIFFRACTIONr_chiral_restr0.0710.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02736
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 96 -
Rwork0.28 1418 -
obs--94.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.4782-1.45730.36793.34190.00192.4272-0.1663-0.39280.38490.40710.1786-0.4163-0.10850.1762-0.01230.0813-0.0099-0.03820.0616-0.03840.1083-63.607570.30158.921
23.2328-0.0852-0.40085.58781.16641.50470.01710.2083-0.4014-0.2907-0.053-0.07620.06880.01350.0360.0375-0.0085-0.00140.0539-0.00840.0934-82.502953.591537.8064
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 179
2X-RAY DIFFRACTION2B3 - 179

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