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- PDB-3vwi: High resolution crystal structure of FraC in the monomeric form -

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Basic information

Entry
Database: PDB / ID: 3vwi
TitleHigh resolution crystal structure of FraC in the monomeric form
ComponentsFragaceatoxin C
KeywordsTOXIN / beta-sandwich / amphipathic alpha-helix / actinoporin / pore-forming toxin / citolysin / Membrane lipids / secreted protein / LIPID RAFT
Function / homology
Function and homology information


nematocyst / cytolysis in another organism / pore complex assembly / 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
AMMONIUM ION / DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesActinia fragacea (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsTanaka, K. / Morante, K. / Caaveiro, J.M.M. / Gonzalez-Manas, J.M. / 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: Structure / Year: 2011
Title: Structural insights into the oligomerization and architecture of eukaryotic membrane pore-forming toxins
Authors: Mechaly, A.E. / Bellomio, A. / Gil-Carton, D. / Morante, K. / Valle, M. / Gonzalez-Manas, J.M. / Guerin, D.M.
History
DepositionAug 23, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,20618
Polymers79,5104
Non-polymers69614
Water13,007722
1
A: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9313
Polymers19,8771
Non-polymers532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2647
Polymers19,8771
Non-polymers3876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9664
Polymers19,8771
Non-polymers893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0444
Polymers19,8771
Non-polymers1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.170, 44.290, 114.710
Angle α, β, γ (deg.)90.000, 92.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Fragaceatoxin C / fraC


Mass: 19877.498 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinia fragacea (sea anemone) / Gene: FraC / Plasmid: pGEM-T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B9W5G6

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Non-polymers , 5 types, 736 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.05 % / Mosaicity: 0.6 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% Jeffamine, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2012
Details: Collimating and focusing mirrors: Rhodium coated silicon single crystals
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→114.573 Å / Num. all: 80105 / Num. obs: 80105 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.792.90.3480.2912.62676091900.1880.3480.2913.375.1
1.79-1.93.30.2510.2123.536105109870.1320.2510.2125.193.4
1.9-2.033.50.1660.1415.236650105770.0860.1660.1417.795.6
2.03-2.193.50.1240.1056.93514499980.0650.1240.1051096.9
2.19-2.43.60.0970.0838.63296092700.0510.0970.08312.597.5
2.4-2.693.60.0820.079.73057784350.0420.0820.0714.897.9
2.69-3.13.70.0660.05610.82792875100.0340.0660.05618.698.6
3.1-3.83.70.0540.04612.22391563800.0280.0540.04623.998.6
3.8-5.383.70.0550.04712.21842049910.0280.0550.04729.498.9
5.38-36.6813.60.0680.0589.3992727670.0350.0680.05829.897.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LIM

3lim


Resolution: 1.7→114.57 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1959 / WRfactor Rwork: 0.1564 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8962 / SU B: 3.604 / SU ML: 0.061 / SU R Cruickshank DPI: 0.096 / SU Rfree: 0.0989 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 3182 4 %RANDOM
Rwork0.1533 ---
all0.1549 80105 --
obs0.1549 80105 93.29 %-
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 max: 60.27 Å2 / Biso mean: 19.4017 Å2 / Biso min: 8.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å2-0.03 Å2
2--0.32 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.7→114.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 32 722 6290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.025882
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.938010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9615767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.21622.768271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60415961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8911544
X-RAY DIFFRACTIONr_chiral_restr0.1590.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024560
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 175 -
Rwork0.202 3976 -
all-4151 -
obs--65.83 %
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)
11.6170.1685-0.21931.2184-0.14341.6955-0.007-0.1533-0.05220.087-0.0156-0.020.0064-0.00910.02260.01550.00240.00240.02450.01120.006826.91890.145612.0713
22.7428-0.4888-0.27140.8313-0.16781.30490.03620.05280.187-0.0309-0.0764-0.0343-0.00030.06620.04020.0130.00230.00290.00930.00620.015613.837818.6943-9.2654
31.28230.30550.31711.55860.46921.9887-0.009-0.0786-0.05290.11630.0053-0.04270.031-0.00070.00370.02830.0019-0.00260.0264-0.00690.007814.42047.9559-45.1453
43.1791-0.41930.11720.85520.16481.19590.04940.1434-0.2262-0.0462-0.09420.03910.0043-0.05730.04480.02680.003-0.00210.0183-0.01740.024927.5623-10.7163-66.4412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 179
2X-RAY DIFFRACTION2B3 - 179
3X-RAY DIFFRACTION3C3 - 179
4X-RAY DIFFRACTION4D3 - 179

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