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- PDB-5bpg: Crystal structure of the water-soluble FraC purified starting fro... -

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Basic information

Entry
Database: PDB / ID: 5bpg
TitleCrystal structure of the water-soluble FraC purified starting from the trans-membrane pore
ComponentsFragaceatoxin C
KeywordsTOXIN / actinoporin / pore-forming toxin / membrane lipids / lipid-protein interaction / protein folding / detergent / protein-detergent 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
DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesActinia fragacea (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsCaaveiro, J.M.M. / Tanaka, K. / Tsumoto, K.
CitationJournal: Biochemistry / Year: 2015
Title: Bidirectional Transformation of a Metamorphic Protein between the Water-Soluble and Transmembrane Native States
Authors: Tanaka, K. / Caaveiro, J.M. / Tsumoto, K.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,03414
Polymers79,5104
Non-polymers52410
Water5,441302
1
A: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9132
Polymers19,8771
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area8060 Å2
MethodPISA
2
B: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0404
Polymers19,8771
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area8050 Å2
MethodPISA
3
C: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0404
Polymers19,8771
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-16 kcal/mol
Surface area8020 Å2
MethodPISA
4
D: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0404
Polymers19,8771
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.300, 44.440, 114.950
Angle α, β, γ (deg.)90.00, 92.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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) / Plasmid: pGEM-T / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B9W5G6
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Microseeds generated in: 24% PEG 4000, 200 mM ammonium sulfate, 100 mM Cacodylate (pH 7.4) Single crystals generated in: 8% PEG 4000, 100 mM TRIS-HCl

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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: Nov 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→47.19 Å / Num. obs: 42232 / % possible obs: 97.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.7
Reflection shellResolution: 2.14→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.4 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
Aimlessphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VWI

3vwi


Resolution: 2.14→47.19 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.859 / SU B: 12.97 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26286 2118 5 %RANDOM
Rwork0.21 ---
obs0.21269 40061 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.627 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20.22 Å2
2--0.12 Å20 Å2
3---1.19 Å2
Refinement stepCycle: 1 / Resolution: 2.14→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 25 302 5863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195695
X-RAY DIFFRACTIONr_bond_other_d0.0010.025345
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9267706
X-RAY DIFFRACTIONr_angle_other_deg0.748312207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3065706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.00622.769260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52115905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.691540
X-RAY DIFFRACTIONr_chiral_restr0.0850.2804
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021453
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_it0.3810.8812830
X-RAY DIFFRACTIONr_mcbond_other0.380.882829
X-RAY DIFFRACTIONr_mcangle_it0.6421.3173531
X-RAY DIFFRACTIONr_mcangle_other0.6421.3173532
X-RAY DIFFRACTIONr_scbond_it0.5330.9482865
X-RAY DIFFRACTIONr_scbond_other0.5320.9482865
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8521.3954175
X-RAY DIFFRACTIONr_long_range_B_refined2.8877.5026612
X-RAY DIFFRACTIONr_long_range_B_other2.7717.3626532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.144→2.2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 117 -
Rwork0.247 2654 -
obs--87.06 %
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)
11.78480.3563-0.10811.6205-0.21182.2142-0.0081-0.1926-0.02150.1463-0.07360.0558-0.0337-0.06560.08170.0159-0.0004-0.00180.0291-0.00440.041626.99230.236712.3554
22.5373-0.0569-0.23650.9444-0.06871.22080.02840.00890.14620.0365-0.0435-0.0504-0.02910.04210.01510.02190.0052-0.01450.0335-0.0020.050814.012418.6387-9.2975
31.44630.49370.29181.80070.48272.73-0.0348-0.0745-0.09280.13440.0172-0.01710.05370.07860.01760.0160.0138-0.00080.04150.00110.05614.40237.8528-44.9634
43.6304-0.2082-0.02451.0472-0.12391.39910.03630.058-0.22980.0149-0.07750.07640.035-0.02930.04120.03180.0047-0.00630.0457-0.0220.088827.546-10.6413-66.574
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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