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- PDB-5imw: Trapped Toxin -

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Basic information

Entry
Database: PDB / ID: 5imw
TitleTrapped Toxin
ComponentsIntermedilysin
KeywordsTOXIN / Locked
Function / homology
Function and homology information


cholesterol binding / toxin activity / killing of cells of another organism / host cell plasma membrane / extracellular region / membrane / metal ion binding
Similarity search - Function
Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin ...Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / Glutaredoxin / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Thiol-activated cytolysin
Similarity search - Component
Biological speciesStreptococcus intermedius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.89 Å
AuthorsLawrence, S.L. / Feil, S.C. / Morton, C.J. / Parker, M.W.
CitationJournal: Structure / Year: 2016
Title: Structural Basis for Receptor Recognition by the Human CD59-Responsive Cholesterol-Dependent Cytolysins.
Authors: Lawrence, S.L. / Gorman, M.A. / Feil, S.C. / Mulhern, T.D. / Kuiper, M.J. / Ratner, A.J. / Tweten, R.K. / Morton, C.J. / Parker, M.W.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intermedilysin
B: Intermedilysin


Theoretical massNumber of molelcules
Total (without water)103,7702
Polymers103,7702
Non-polymers00
Water0
1
A: Intermedilysin


Theoretical massNumber of molelcules
Total (without water)51,8851
Polymers51,8851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Intermedilysin


Theoretical massNumber of molelcules
Total (without water)51,8851
Polymers51,8851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.465, 101.565, 175.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Intermedilysin


Mass: 51885.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus intermedius (bacteria) / Gene: ily / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LCB8

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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: 3.66 Å3/Da / Density % sol: 66.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MES, NaCl, PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.89→48.135 Å / Num. obs: 34453 / % possible obs: 98.8 % / Redundancy: 14.6 % / Net I/σ(I): 10.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S3R

1s3r


Resolution: 2.89→48.135 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.295 1728 5.06 %
Rwork0.2584 --
obs0.2603 34136 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→48.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7113 0 0 0 7113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037262
X-RAY DIFFRACTIONf_angle_d0.549858
X-RAY DIFFRACTIONf_dihedral_angle_d14.4454367
X-RAY DIFFRACTIONf_chiral_restr0.0431116
X-RAY DIFFRACTIONf_plane_restr0.0031267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8898-2.97480.4591200.40712426X-RAY DIFFRACTION90
2.9748-3.07080.35841590.3892684X-RAY DIFFRACTION99
3.0708-3.18050.38781540.36192635X-RAY DIFFRACTION99
3.1805-3.30780.34541450.30922657X-RAY DIFFRACTION99
3.3078-3.45840.35261340.27952693X-RAY DIFFRACTION99
3.4584-3.64060.29141410.282712X-RAY DIFFRACTION100
3.6406-3.86860.29761370.26742725X-RAY DIFFRACTION100
3.8686-4.16720.33351480.26492690X-RAY DIFFRACTION99
4.1672-4.58620.24821610.2362714X-RAY DIFFRACTION99
4.5862-5.24920.26341270.22112764X-RAY DIFFRACTION100
5.2492-6.61070.31681500.25012788X-RAY DIFFRACTION100
6.6107-48.14190.23981520.21652920X-RAY DIFFRACTION100

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