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- PDB-1gwy: Crystal structure of the water-soluble state of the pore-forming ... -

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Basic information

Entry
Database: PDB / ID: 1gwy
TitleCrystal structure of the water-soluble state of the pore-forming cytolysin Sticholysin II
ComponentsSTICHOLYSIN II
KeywordsCYTOLYSIN / PORE-FORMING TOXIN / HEMOLYSIS / CNIDOCYST
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 / 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-stichotoxin-She4b
Similarity search - Component
Biological speciesSTOICHACTIS HELIANTHUS (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsMancheno, J.M. / Martin-Benito, J. / Martinez-Ripoll, M. / Gavilanes, J.G. / Hermoso, J.A.
CitationJournal: Structure / Year: 2003
Title: Crystal and Electron Microscopy Structures of Sticholysin II Actinoporin Reveal Insights Into the Mechanism of Membrane Pore Formation
Authors: Mancheno, J.M. / Martin-Benito, J. / Martinez-Ripoll, M. / Gavilanes, J.G. / Hermoso, J.A.
History
DepositionMar 26, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STICHOLYSIN II
B: STICHOLYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,37410
Polymers38,6062
Non-polymers7698
Water6,720373
1
A: STICHOLYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5914
Polymers19,3031
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: STICHOLYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7836
Polymers19,3031
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.304, 119.735, 43.421
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein STICHOLYSIN II / CYTOLYSIN III / CYTOLYSIN ST II / CYTOTOXIN


Mass: 19302.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) STOICHACTIS HELIANTHUS (sea anemone) / References: UniProt: P07845
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.13 Å3/Da / Density % sol: 42 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMTris1droppH7.0
26-8 mg/mlprotein1drop
30.2 Mlithium sulfate1reservoir
40.1 MTris1reservoirpH7.5
525-30 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0004
DetectorDetector: CCD / Date: May 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0004 Å / Relative weight: 1
ReflectionResolution: 1.71→32.27 Å / Num. obs: 31889 / % possible obs: 90.3 % / Observed criterion σ(I): 4 / Redundancy: 2.1 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 5
Reflection shellResolution: 1.71→1.81 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.151 / % possible all: 90.3
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 32.3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.086

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1IAZ

1iaz


Resolution: 1.71→9.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 714940.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE ELECTRON DENSITY OF THE LOOP REGION COMPRISED BETWEEN RESIDUES 109-111 IS NOT WELL DEFINED, PRESUMABLY DUE TO A HIGH MOBILITY. THE OCUPATION AND B FACTORS OF THE TRP-110 SIDE CHAIN HAVE ...Details: THE ELECTRON DENSITY OF THE LOOP REGION COMPRISED BETWEEN RESIDUES 109-111 IS NOT WELL DEFINED, PRESUMABLY DUE TO A HIGH MOBILITY. THE OCUPATION AND B FACTORS OF THE TRP-110 SIDE CHAIN HAVE BEEN SET TO 0.00 AND 20.00, RESPECTIVELY, DUE TO THE POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1578 5 %RANDOM
Rwork0.216 ---
obs0.216 31683 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.759 Å2 / ksol: 0.428738 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2--0.23 Å20 Å2
3---0.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.71→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 40 373 3135
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.62
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.71→1.82 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 191 4.9 %
Rwork0.282 3707 -
obs--65.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.62

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