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- PDB-5gwf: FraC with GlcNAc(6S) bound -

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Basic information

Entry
Database: PDB / ID: 5gwf
TitleFraC with GlcNAc(6S) bound
ComponentsDELTA-actitoxin-Afr1a
KeywordsTOXIN / ACTINOPORIN / PORE-FORMING TOXIN / CARBOHYDRATE-PROTEIN INTERACTION / LIPID-PROTEIN INTERACTION / CYTOLYSIN / NANOPORE
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
Chem-NGY / DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesActinia fragacea (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCaaveiro, J.M.M. / Tsumoto, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS25249115 Japan
JSPS15K06962 Japan
CitationJournal: Philos. Trans. R. Soc. Lond., B, Biol. Sci. / Year: 2017
Title: Haemolytic actinoporins interact with carbohydrates using their lipid-binding module
Authors: Tanaka, K. / Caaveiro, J.M.M. / Morante, K. / Tsumoto, K.
History
DepositionSep 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: DELTA-actitoxin-Afr1a
B: DELTA-actitoxin-Afr1a
C: DELTA-actitoxin-Afr1a
D: DELTA-actitoxin-Afr1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,75821
Polymers79,5104
Non-polymers1,24817
Water13,727762
1
A: DELTA-actitoxin-Afr1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9132
Polymers19,8771
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8070 Å2
MethodPISA
2
B: DELTA-actitoxin-Afr1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4849
Polymers19,8771
Non-polymers6068
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area8090 Å2
MethodPISA
3
C: DELTA-actitoxin-Afr1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0765
Polymers19,8771
Non-polymers1984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area8020 Å2
MethodPISA
4
D: DELTA-actitoxin-Afr1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2855
Polymers19,8771
Non-polymers4084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 44.400, 114.360
Angle α, β, γ (deg.)90.00, 92.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DELTA-actitoxin-Afr1a / DELTA-AITX-Afr1a / Cytolysin 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) / 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.: 13 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-NGY / 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose / 2-(acetylamino)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose / N-acetyl-6-O-sulfo-alpha-D-glucosamine / 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-glucose


Type: D-saccharide, alpha linking / Mass: 301.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO9S
IdentifierTypeProgram
DGlcpNAc[6S]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-6-sulfo-a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpNAc6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 762 / 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: 50.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 18% PEG8000, 210mM ammonium sulfate, 100mM sodium cacodylate

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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 270 / Detector: CCD / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→37.06 Å / Num. obs: 103405 / % possible obs: 91.8 % / Redundancy: 5.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.8
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.5 / CC1/2: 0.937 / % possible all: 76.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLM7.1.0data reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VWI

3vwi


Resolution: 1.55→37.06 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.307 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16307 3161 3.1 %RANDOM
Rwork0.11761 ---
obs0.11895 100243 91.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.022 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.53 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.55→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 63 762 6361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195909
X-RAY DIFFRACTIONr_bond_other_d0.0020.025541
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9348061
X-RAY DIFFRACTIONr_angle_other_deg0.995312712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9325772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.49822.889270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08715947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4171542
X-RAY DIFFRACTIONr_chiral_restr0.1010.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026875
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021505
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_it1.4621.3222908
X-RAY DIFFRACTIONr_mcbond_other1.461.3192903
X-RAY DIFFRACTIONr_mcangle_it1.6561.9813645
X-RAY DIFFRACTIONr_mcangle_other1.6571.9813644
X-RAY DIFFRACTIONr_scbond_it2.341.6333001
X-RAY DIFFRACTIONr_scbond_other2.3391.6333001
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6272.3414384
X-RAY DIFFRACTIONr_long_range_B_refined3.05212.5767247
X-RAY DIFFRACTIONr_long_range_B_other2.6411.8246853
X-RAY DIFFRACTIONr_rigid_bond_restr3.953311450
X-RAY DIFFRACTIONr_sphericity_free18.2275259
X-RAY DIFFRACTIONr_sphericity_bonded5.979511808
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.173 189 -
Rwork0.134 5617 -
obs--69.6 %

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