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- PDB-3zx7: Complex of lysenin with phosphocholine -

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Basic information

Entry
Database: PDB / ID: 3zx7
TitleComplex of lysenin with phosphocholine
ComponentsLYSENIN
KeywordsTOXIN / PORE FORMING TOXIN
Function / homology
Function and homology information


other organism cell membrane / monoatomic ion transport / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region / membrane
Similarity search - Function
Jelly Rolls - #980 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHOCHOLINE / PHOSPHATE ION / Lysenin
Similarity search - Component
Biological speciesEISENIA FETIDA (common brandling worm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.84 Å
AuthorsDe Colibus, L. / Sonnen, A.F.P. / Morris, K.J. / Siebert, C.A. / Abrusci, P. / Plitzko, J. / Hodnik, V. / Leippe, M. / Volpi, E. / Anderluh, G. / Gilbert, R.J.C.
CitationJournal: Structure / Year: 2012
Title: Structures of Lysenin Reveal a Shared Evolutionary Origin for Pore-Forming Proteins and its Mode of Sphingomyelin Recognition.
Authors: De Colibus, L. / Sonnen, A.F.P. / Morris, K.J. / Siebert, C.A. / Abrusci, P. / Plitzko, J. / Hodnik, V. / Leippe, M. / Volpi, E. / Anderluh, G. / Gilbert, R.J.C.
History
DepositionAug 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,40813
Polymers35,1271
Non-polymers1,28012
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.110, 98.110, 184.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein LYSENIN


Mass: 35127.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EISENIA FETIDA (common brandling worm) / Tissue: COELOMIC FLUID / Plasmid: PTETLYS1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O18423
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H15NO4P
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.68 Å3/Da / Density % sol: 66.61 % / Description: NONE
Crystal growpH: 4.5
Details: 1.8 M AMMONIUM DI-HYDROGEN PHOSPHATE, 1.0 M SODIUM ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97867
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 18, 2007 / Details: BENT COLLIMATING MIRROR AND TOROID
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97867 Å / Relative weight: 1
ReflectionResolution: 2.8→32.1 Å / Num. obs: 12994 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 22.1 % / Biso Wilson estimate: 72.61 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 29
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 23 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 4.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.84→23.7 Å / Cor.coef. Fo:Fc: 0.8919 / Cor.coef. Fo:Fc free: 0.8532 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.628 / SU Rfree Blow DPI: 0.33
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=PO4 PC. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4713. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=58. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=PO4 PC. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4713. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=58. NUMBER TREATED BY BAD NON-BONDED CONTACTS=6.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 630 4.87 %RANDOM
Rwork0.2235 ---
obs0.2255 12930 99.57 %-
Displacement parametersBiso mean: 75.88 Å2
Baniso -1Baniso -2Baniso -3
1--3.3721 Å20 Å20 Å2
2---3.3721 Å20 Å2
3---6.7443 Å2
Refine analyzeLuzzati coordinate error obs: 0.499 Å
Refinement stepCycle: LAST / Resolution: 2.84→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 72 24 2451
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094770HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.118576HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1037SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes698HARMONIC5
X-RAY DIFFRACTIONt_it4770HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion18.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion323SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5048SEMIHARMONIC4
LS refinement shellResolution: 2.84→3.07 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3229 133 5.18 %
Rwork0.2286 2435 -
all0.2335 2568 -
obs--99.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
112.83212.4157-0.13971.2612-2.01320-0.2110.0907-0.21620.10330.3763-1.60830.0050.6495-0.1653-0.1330.0349-0.1579-0.4334-0.29360.348436.991310.908415.2861
2-0.11550.49140.37960.6059-1.57380-0.22870.29490.0611-0.03990.101-0.53920.2048-0.11440.1277-0.3839-0.09190.0744-0.0269-0.45290.635258.613221.79524.3616
36.77623.97922.20748.24726.82569.0139-0.11560.9431-0.3629-0.07870.1539-1.2146-0.0118-0.5225-0.0383-0.42420.1324-0.1354-0.2475-0.1105-0.000930.728713.957110.881
46.8949-0.0401-1.06410.3761.75312.9648-0.22120.2427-0.3622-0.261-0.2602-0.0240.1980.19320.4815-0.25450.227-0.0545-0.2229-0.2960.639952.512216.396512.8242
5-2.760.743-1.952513.4924-5.36951.45810.03840.0624-0.3023-0.13590.32020.3283-0.13740.1293-0.3586-0.19180.45020.29710.34130.11110.547163.71729.866910.4798
6-2.92853.28373.21476.68836.32710.36730.05660.0516-0.0405-0.1242-0.1538-0.02810.249-0.03370.09730.30110.1539-0.4426-0.1409-0.14530.729442.4526.480819.0233
71.752-0.14451.55692.71070.16555.6395-0.0354-0.19590.33840.4458-0.33010.0561-0.2518-0.60240.36550.08350.0443-0.039-0.1338-0.1257-0.26825.274114.38949.0919
82.65071.99632.49646.86640.51385.9942-0.20720.17560.7188-0.0906-0.1854-0.2316-1.2995-0.33170.39260.08750.1041-0.1652-0.1687-0.0214-0.26624.368622.3767-2.2726
92.239-1.97960.46140.14050.08370.1119-0.1670.09060.29980.2492-0.1408-0.00990.1744-0.21780.30780.29760.0114-0.1044-0.169-0.0426-0.118911.830817.967813.1992
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 6:22
2X-RAY DIFFRACTION2CHAIN A AND RESID 23:48
3X-RAY DIFFRACTION3CHAIN A AND RESID 49:75
4X-RAY DIFFRACTION4CHAIN A AND RESID 76:131
5X-RAY DIFFRACTION5CHAIN A AND RESID 132:147
6X-RAY DIFFRACTION6CHAIN A AND RESID 148:154
7X-RAY DIFFRACTION7CHAIN A AND RESID 155:267
8X-RAY DIFFRACTION8CHAIN A AND RESID 268:286
9X-RAY DIFFRACTION9CHAIN A AND RESID 287:992

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