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- PDB-4tsp: Crystal structure of FraC with DHPC bound (crystal form II) -

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Basic information

Entry
Database: PDB / ID: 4tsp
TitleCrystal structure of FraC with DHPC bound (crystal form II)
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 / PHOSPHOCHOLINE / PHOSPHATE ION / DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesActinia fragacea (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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)42,44817
Polymers39,4932
Non-polymers2,95515
Water2,090116
1
A: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9416
Polymers19,7461
Non-polymers1,1955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,50611
Polymers19,7461
Non-polymers1,76010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.550, 129.550, 49.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-207-

PO4

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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 , 5 types, 131 molecules

#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.: 4 / 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.: 7 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#6: 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: 2.61 Å3/Da / Density % sol: 52.91 %
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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→35.93 Å / Num. obs: 22701 / % possible obs: 97.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 6.5
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / % possible all: 79.7

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Processing

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

3vwi


Resolution: 2.15→35.93 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.347 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24744 1167 5.1 %RANDOM
Rwork0.20008 ---
obs0.20238 21505 97 %-
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: 33.266 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2---1.57 Å20 Å2
3---3.15 Å2
Refinement stepCycle: 1 / Resolution: 2.15→35.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 181 116 3065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023028
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212862
X-RAY DIFFRACTIONr_angle_refined_deg1.981.984101
X-RAY DIFFRACTIONr_angle_other_deg1.2643.0196541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8645358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.46422.632133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24715459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3861522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023345
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02737
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: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 101 -
Rwork0.264 1595 -
obs--99.41 %
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)
15.5177-1.4085-0.34921.50020.20651.6398-0.11-0.2076-0.14440.09190.0669-0.04420.08910.02680.0430.2044-0.00320.01060.16790.01430.0118-46.2057-11.47049.1487
22.70560.1803-0.27016.8581-1.86322.24470.02770.18350.2657-0.1882-0.1244-0.216-0.19760.14640.09670.1970.0192-0.00040.25080.02010.0364-22.7561-1.8795-10.943
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 179
2X-RAY DIFFRACTION2B3 - 179

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