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- PDB-4tw1: Crystal structure of the octameric pore complex of the Staphyloco... -

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Basic information

Entry
Database: PDB / ID: 4tw1
TitleCrystal structure of the octameric pore complex of the Staphylococcus aureus Bi-component Toxin LukGH
Components(Possible leukocidin subunit) x 2
KeywordsTOXIN / octamer leukocidin pore-forming toxin
Function / homologyLeukocidin/porin MspA / Leukocidin-like / Distorted Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsLogan, D.T. / Hakansson, M. / Saline, M. / Kimbung, R. / Badarau, A. / Rouha, H. / Nagy, E.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure-Function Analysis of Heterodimer Formation, Oligomerization, and Receptor Binding of the Staphylococcus aureus Bi-component Toxin LukGH.
Authors: Badarau, A. / Rouha, H. / Malafa, S. / Logan, D.T. / Hakansson, M. / Stulik, L. / Dolezilkova, I. / Teubenbacher, A. / Gross, K. / Maierhofer, B. / Weber, S. / Jagerhofer, M. / Hoffman, D. / Nagy, E.
History
DepositionJun 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Apr 8, 2015Group: Derived calculations
Revision 1.4Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jun 12, 2019Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.6Dec 20, 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 / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Possible leukocidin subunit
B: Possible leukocidin subunit
C: Possible leukocidin subunit
D: Possible leukocidin subunit
E: Possible leukocidin subunit
F: Possible leukocidin subunit
G: Possible leukocidin subunit
H: Possible leukocidin subunit
I: Possible leukocidin subunit
J: Possible leukocidin subunit
K: Possible leukocidin subunit
L: Possible leukocidin subunit
M: Possible leukocidin subunit
N: Possible leukocidin subunit
O: Possible leukocidin subunit
P: Possible leukocidin subunit


Theoretical massNumber of molelcules
Total (without water)588,06616
Polymers588,06616
Non-polymers00
Water3,693205
1
A: Possible leukocidin subunit
B: Possible leukocidin subunit
C: Possible leukocidin subunit
D: Possible leukocidin subunit
E: Possible leukocidin subunit
F: Possible leukocidin subunit
G: Possible leukocidin subunit
H: Possible leukocidin subunit


Theoretical massNumber of molelcules
Total (without water)294,0338
Polymers294,0338
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37620 Å2
ΔGint-49 kcal/mol
Surface area93190 Å2
MethodPISA
2
I: Possible leukocidin subunit
J: Possible leukocidin subunit
K: Possible leukocidin subunit
L: Possible leukocidin subunit
M: Possible leukocidin subunit
N: Possible leukocidin subunit
O: Possible leukocidin subunit
P: Possible leukocidin subunit


Theoretical massNumber of molelcules
Total (without water)294,0338
Polymers294,0338
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37790 Å2
ΔGint-56 kcal/mol
Surface area93450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.497, 198.558, 179.535
Angle α, β, γ (deg.)90.000, 103.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Possible leukocidin subunit / LUKG


Mass: 35825.539 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: USA300 / TCH1516 / Gene: USA300HOU_2011 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta, Tuner / References: UniProt: A8Z4S0
#2: Protein
Possible leukocidin subunit / LUKH


Mass: 37682.680 Da / Num. of mol.: 8 / Fragment: Residues 28-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: USA300 / TCH1516 / Gene: USA300HOU_2013 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta, Tuner / References: UniProt: A8Z4S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 4.39 Å3/Da / Density % sol: 71.96 % / Description: Thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Drops consisted of 100 nl protein in 20 mM HEPES buffer pH 7.5 and 100 nl reservoir 30 mM MgCl2, 30 mM CaCl2, 0.1 M Na HEPES/MOPS buffer pH 7.5, 12.5 % v/v MPD, 12.5 % w/v PEG 1000, 12.5 % ...Details: Drops consisted of 100 nl protein in 20 mM HEPES buffer pH 7.5 and 100 nl reservoir 30 mM MgCl2, 30 mM CaCl2, 0.1 M Na HEPES/MOPS buffer pH 7.5, 12.5 % v/v MPD, 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350. Crystals appeared after 7 days.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2013
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.188 Å / Num. all: 222018 / Num. obs: 222018 / % possible obs: 97.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 56.4 Å2 / Rpim(I) all: 0.109 / Rrim(I) all: 0.194 / Rsym value: 0.16 / Net I/av σ(I): 4.824 / Net I/σ(I): 10.1 / Num. measured all: 685808
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.953.10.8710.996878315570.5910.8711.795.4
2.95-3.133.10.5721.495716307140.3860.5722.698.3
3.13-3.343.10.3542.390326289940.2390.3544.198.5
3.34-3.613.10.2043.984102269770.1380.2046.898.4
3.61-3.953.10.1425.677132248210.0960.1429.498.6
3.95-4.423.10.0849.569405224750.0570.08414.998.5
4.42-5.113.10.05913.661181198660.040.0592098.5
5.11-6.253.10.07310.951663167570.050.07316.798.5
6.25-8.8430.05115.239428129810.0360.05122.298.4
8.84-48.1882.90.02429.81997768760.0170.0244194.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.3 Å48.19 Å
Translation7.3 Å48.19 Å

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Processing

Software
NameVersionClassification
XDS2.5.5data reduction
SCALA3.3.21data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
REFMAC5.8.0073refinement
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B07 prepared using CHAINSAW

3b07


Resolution: 2.8→48 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.856 / WRfactor Rfree: 0.2318 / WRfactor Rwork: 0.1798 / FOM work R set: 0.6812 / SU B: 20.998 / SU ML: 0.362 / SU R Cruickshank DPI: 0.512 / SU Rfree: 0.3468 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.512 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2923 2207 1 %RANDOM
Rwork0.2381 216290 --
obs0.2387 218497 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.12 Å2 / Biso mean: 36.001 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-4.69 Å20 Å2-3.36 Å2
2---1.99 Å20 Å2
3----1.01 Å2
Refinement stepCycle: final / Resolution: 2.8→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37415 0 0 205 37620
Biso mean---17.55 -
Num. residues----4576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01938286
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.9351726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.10954550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49124.9632005
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.748156829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.72115180
X-RAY DIFFRACTIONr_chiral_restr0.1120.25427
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02129365
X-RAY DIFFRACTIONr_mcbond_it2.3183.45518278
X-RAY DIFFRACTIONr_mcangle_it3.8875.17222802
X-RAY DIFFRACTIONr_scbond_it2.6963.71420008
LS refinement shellResolution: 2.8→2.869 Å
RfactorNum. reflection% reflection
Rfree0.482 174 1 %
Rwork0.435 14319 -
obs--86.53 %

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