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- PDB-4hsc: Crystal structure of a cholesterol dependent cytolysin -

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Basic information

Entry
Database: PDB / ID: 4hsc
TitleCrystal structure of a cholesterol dependent cytolysin
ComponentsStreptolysin O
KeywordsTOXIN / cholesterol-dependent cytolysins / membrane insertion / membrane pore / pore-forming toxins / pore-forming toxin
Function / homology
Function and homology information


hemolysis in another organism / cholesterol binding / : / toxin activity / membrane => GO:0016020 / host cell plasma membrane / extracellular region
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 cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain ...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 cytolysins signature. / 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
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsFeil, S.C. / Parker, M.W.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural studies of Streptococcus pyogenes streptolysin O provide insights into the early steps of membrane penetration.
Authors: Feil, S.C. / Ascher, D.B. / Kuiper, M.J. / Tweten, R.K. / Parker, M.W.
History
DepositionOct 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 20, 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

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Assembly

Deposited unit
X: Streptolysin O


Theoretical massNumber of molelcules
Total (without water)63,7201
Polymers63,7201
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.208, 85.343, 81.223
Angle α, β, γ (deg.)90.000, 92.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Streptolysin O / Thiol-activated cytolysin


Mass: 63720.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: SSI-1 / Gene: slo, SPs0132 / Plasmid: prT20 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 Blue / References: UniProt: P0DF97, NAD+ glycohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 8000, 20 mM CaCl2, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2005 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→58.82 Å / Num. all: 36851 / Num. obs: 35414 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.82 % / Rmerge(I) obs: 0.063 / Χ2: 0.99 / Net I/σ(I): 9.6 / Scaling rejects: 1024
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.1-2.183.830.4012.61321834271.3494.6
2.18-2.263.850.3522.91352534971.2694.7
2.26-2.373.850.2943.41355235041.1895.2
2.37-2.493.840.2354.31344434921.1395.8
2.49-2.653.840.1785.41361835281.0596.1
2.65-2.853.860.127.51381335650.9496.2
2.85-3.143.860.07710.91381635660.8397
3.14-3.593.840.048161391036100.7697.6
3.59-4.523.810.03821.21386936240.7297.9
4.52-58.823.640.04421.11359036010.7395.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
d*TREK9.4SSIdata reduction
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PFO

1pfo


Resolution: 2.1→40.585 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7724 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 1766 5 %Random
Rwork0.2215 ---
obs0.2237 35338 95.94 %-
all-36848 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.327 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 88.89 Å2 / Biso mean: 43.1297 Å2 / Biso min: 19.77 Å2
Baniso -1Baniso -2Baniso -3
1-3.335 Å2-0 Å20.6293 Å2
2---0.0219 Å20 Å2
3----3.3131 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 0 150 3842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083764
X-RAY DIFFRACTIONf_angle_d1.1555110
X-RAY DIFFRACTIONf_chiral_restr0.081581
X-RAY DIFFRACTIONf_plane_restr0.005659
X-RAY DIFFRACTIONf_dihedral_angle_d19.9491366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15680.40651320.32092518265095
2.1568-2.22020.3611230.29662524264794
2.2202-2.29190.3561360.26382551268795
2.2919-2.37380.32591270.25882556268395
2.3738-2.46880.33391310.25032586271796
2.4688-2.58120.28921220.25312567268995
2.5812-2.71720.34391370.25272602273996
2.7172-2.88740.28571480.23652581272997
2.8874-3.11030.29911410.24662605274698
3.1103-3.42310.25651340.22412631276598
3.4231-3.91810.24541610.1992626278797
3.9181-4.93510.19191360.16622642277898
4.9351-40.59220.21191380.17212583272193

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