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- PDB-4tsl: Crystal structure of FraC with POC bound (crystal form I) -

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Basic information

Entry
Database: PDB / ID: 4tsl
TitleCrystal structure of FraC with POC 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
ACETATE ION / FORMIC ACID / PHOSPHOCHOLINE / DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesActinia fragacea (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,03320
Polymers39,4932
Non-polymers1,54018
Water6,449358
1
A: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,49610
Polymers19,7461
Non-polymers7509
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-7 kcal/mol
Surface area8440 Å2
MethodPISA
2
B: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,53710
Polymers19,7461
Non-polymers7919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-6 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.740, 64.740, 219.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-351-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 376 molecules

#2: Chemical
ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H15NO4P
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM POC, 3 mM DDM, 200 mM Li2SO4, 100 mM ammonium formate, 24% PEG 8000, 100 sodium acetate
PH range: 4.1 - 4.3

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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: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→32.37 Å / Num. obs: 62950 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 14.34 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 17.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

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

3vwi


Resolution: 1.6→32.37 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.246 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17238 1910 3 %RANDOM
Rwork0.1488 ---
obs0.14954 60922 99.94 %-
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: 18.817 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.6→32.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 94 358 3230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193118
X-RAY DIFFRACTIONr_bond_other_d0.0010.022967
X-RAY DIFFRACTIONr_angle_refined_deg2.3361.964254
X-RAY DIFFRACTIONr_angle_other_deg0.90236796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.725406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.95122.695141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83515499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3161524
X-RAY DIFFRACTIONr_chiral_restr0.1360.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023572
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02792
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: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 135 -
Rwork0.241 4415 -
obs--100 %
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)
12.10310.46220.45281.25450.36412.07830.0321-0.1168-0.11180.02910.0198-0.07890.12690.102-0.0520.02480.019-0.00910.04840.00950.01519.596263.359617.5318
21.4031-0.2682-0.13491.6290.49051.7844-0.0085-0.1299-0.01070.03340.03890.19890.0318-0.1368-0.03040.0034-0.0080.00190.07720.02390.0331-7.154371.437315.721
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 179
2X-RAY DIFFRACTION2B2 - 179

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