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- PDB-4tsq: Crystal structure of FraC with DHPC bound (crystal form III) -

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Basic information

Entry
Database: PDB / ID: 4tsq
TitleCrystal structure of FraC with DHPC bound (crystal form III)
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 / channel activity / pore complex / monoatomic cation transport / 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 / THIOCYANATE ION / 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
C: Fragaceatoxin C
D: Fragaceatoxin C
E: Fragaceatoxin C
F: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,58537
Polymers118,4786
Non-polymers9,10731
Water15,439857
1
A: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4459
Polymers19,7461
Non-polymers2,6998
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8690 Å2
MethodPISA
2
B: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6587
Polymers19,7461
Non-polymers1,9126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area8610 Å2
MethodPISA
3
C: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8394
Polymers19,7461
Non-polymers1,0933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8270 Å2
MethodPISA
4
D: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8985
Polymers19,7461
Non-polymers1,1514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8440 Å2
MethodPISA
5
E: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1177
Polymers19,7461
Non-polymers1,3716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8920 Å2
MethodPISA
6
F: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6275
Polymers19,7461
Non-polymers8814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.270, 70.270, 202.973
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Fragaceatoxin C / fraC


Mass: 19746.303 Da / Num. of mol.: 6
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, 888 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.: 16 / Source method: obtained synthetically / Formula: C20H41NO8P
#3: Chemical
ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H15NO4P
#4: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium thiocyanate, 20% PEG 3350, 30 mM DHPC, 3 mM dehydroepiandrosterone
PH range: 6.9

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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 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.833
11K, H, -L20.167
ReflectionResolution: 1.6→45.25 Å / Num. obs: 141157 / % possible obs: 95.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 17
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 5 / % possible all: 77.1

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VWI

3vwi


Resolution: 1.6→45.25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.414 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15419 4325 3.1 %RANDOM
Rwork0.13198 ---
obs0.13265 136751 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.734 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å20 Å2
2--2.05 Å20 Å2
3----4.1 Å2
Refinement stepCycle: 1 / Resolution: 1.6→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8319 0 585 857 9761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.029380
X-RAY DIFFRACTIONr_bond_other_d0.0070.0219106
X-RAY DIFFRACTIONr_angle_refined_deg2.1461.98512720
X-RAY DIFFRACTIONr_angle_other_deg1.4463.02520853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.130.21311
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022272
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_it0.9220.914345
X-RAY DIFFRACTIONr_mcbond_other0.890.9094339
X-RAY DIFFRACTIONr_mcangle_it1.3421.3615436
X-RAY DIFFRACTIONr_mcangle_other1.3421.3625437
X-RAY DIFFRACTIONr_scbond_it2.1831.4765035
X-RAY DIFFRACTIONr_scbond_other2.1761.4765031
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4552.0557242
X-RAY DIFFRACTIONr_long_range_B_refined5.98412.0168150
X-RAY DIFFRACTIONr_long_range_B_other5.91311.3857792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 244 -
Rwork0.188 7641 -
obs--72.46 %
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)
11.0647-0.1655-0.06592.015-0.51981.12420.00430.04420-0.072-0.0714-0.04020.12960.08420.06710.03350.03370.02150.03880.02190.018-6.432512.33969.9805
22.1937-1.1091-0.26962.2903-0.45811.11730.060.06690.0250.0535-0.00630.0615-0.14190.0046-0.05380.07620.0190.02130.01060.01440.053713.0654-17.02439.7815
32.5676-0.43650.07621.3234-0.51761.72810.0064-0.1177-0.04830.03660.0070.03340.0877-0.0975-0.01330.0087-0.0078-0.00440.02950.0060.044125.72217.6158-13.6853
41.9526-0.67950.18152.0215-0.03431.2373-0.0435-0.07090.00950.07240.03820.0977-0.0519-0.02170.00530.04010.0144-0.01720.0077-0.01080.03877.1953-12.1528-23.0529
51.309-0.3155-0.05682.8597-0.16170.98960.04040.0677-0.0564-0.075-0.0257-0.07060.02770.1007-0.01470.01330.0235-0.01020.0504-0.01850.0346-8.339619.0225-23.1481
62.2555-0.69551.33621.1598-1.18783.90580.13660.173-0.0605-0.0266-0.03420.19570.0349-0.0128-0.10240.03970.02030.00760.0502-0.00650.078531.529218.154720.5292
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 179
2X-RAY DIFFRACTION2B2 - 179
3X-RAY DIFFRACTION3C3 - 179
4X-RAY DIFFRACTION4D2 - 179
5X-RAY DIFFRACTION5E2 - 179
6X-RAY DIFFRACTION6F3 - 179

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