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- PDB-3w9p: Crystal structure of monomeric FraC (second crystal form) -

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Basic information

Entry
Database: PDB / ID: 3w9p
TitleCrystal structure of monomeric FraC (second crystal form)
ComponentsFragaceatoxin C
KeywordsTOXIN / beta-sandwich / amphipathic alpha-helix / actinoporin / pore-forming toxin / cytolysin / membrane lipids / secreted protein
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
DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesActinia fragacea (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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: 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
DepositionApr 9, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fragaceatoxin C
B: Fragaceatoxin C


Theoretical massNumber of molelcules
Total (without water)39,7552
Polymers39,7552
Non-polymers00
Water2,648147
1
A: Fragaceatoxin C


Theoretical massNumber of molelcules
Total (without water)19,8771
Polymers19,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fragaceatoxin C


Theoretical massNumber of molelcules
Total (without water)19,8771
Polymers19,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.980, 60.510, 80.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fragaceatoxin C / fraC


Mass: 19877.498 Da / Num. of mol.: 2
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.81 Å3/Da / Density % sol: 32.2 % / Mosaicity: 1.089 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM sodium citrate, 20% isopropanol, 16% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→42.27 Å / Num. all: 17493 / Num. obs: 17493 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2498 / Rsym value: 0.366 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.13 Å42.24 Å
Translation4.13 Å42.24 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
XSCALEdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LIM

3lim


Resolution: 2.1→42.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.1938 / WRfactor Rwork: 0.1468 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8862 / SU B: 4.605 / SU ML: 0.123 / SU R Cruickshank DPI: 0.2634 / SU Rfree: 0.1926 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 883 5.1 %RANDOM
Rwork0.1619 ---
all0.1646 17493 --
obs0.1646 17450 99.98 %-
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: 61.15 Å2 / Biso mean: 20.6013 Å2 / Biso min: 9.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--1.45 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 0 147 2880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192819
X-RAY DIFFRACTIONr_bond_other_d0.0010.022650
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9243821
X-RAY DIFFRACTIONr_angle_other_deg0.74336054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2095353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85122.713129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30715451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0651520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02724
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 54 -
Rwork0.188 1194 -
all-1248 -
obs-1194 99.92 %

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