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- PDB-3zxd: wild-type lysenin -

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Basic information

Entry
Database: PDB / ID: 3zxd
Titlewild-type lysenin
ComponentsLYSENIN
KeywordsTOXIN / PORE FORMING TOXIN / EARTHWORM
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
Biological speciesEISENIA FETIDA (common brandling worm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSENIN
B: LYSENIN
C: LYSENIN
D: LYSENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,05028
Polymers139,3844
Non-polymers1,66624
Water1448
1
A: LYSENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,47711
Polymers34,8461
Non-polymers63110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4018
Polymers34,8461
Non-polymers5557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LYSENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9874
Polymers34,8461
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LYSENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1855
Polymers34,8461
Non-polymers3394
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.910, 85.560, 108.810
Angle α, β, γ (deg.)98.88, 96.84, 90.04
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1, -0.00139, -0.00176), (-0.00139, -1, -0.00228), (-0.00176, 0.00228, -1)29.4951, -17.95526, -23.40585
2given(-0.09731, -0.42236, 0.90199), (-0.1457, -0.88969, -0.4327), (0.98453, -0.17341, 0.02504)-13.40506, -39.91133, 24.04018
3given(-0.22469, -0.41298, 0.88259), (0.18757, 0.87048, 0.45506), (-0.95621, 0.26779, -0.11813)13.60263, 22.70005, -50.02237

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
LYSENIN / EFL1


Mass: 34846.051 Da / Num. of mol.: 4
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

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Non-polymers , 7 types, 32 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.87 Å3/Da / Density % sol: 68.24 % / Description: NONE
Crystal growpH: 6.5 / Details: 1M MES, 1.6M MAGNESIUM SULFATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 2007 / Details: BENT COLLIMATING MIRROR AND TOROID
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.3→44.36 Å / Num. obs: 30603 / % possible obs: 97.8 % / Observed criterion σ(I): 6 / Redundancy: 3.5 % / Biso Wilson estimate: 46.18 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.3
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.8 / % possible all: 97.4

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZX7

3zx7


Resolution: 3.3→29.09 Å / Cor.coef. Fo:Fc: 0.8578 / Cor.coef. Fo:Fc free: 0.8338 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.411
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1539 5.03 %RANDOM
Rwork0.213 ---
obs0.2142 30580 97.72 %-
Displacement parametersBiso mean: 69.26 Å2
Baniso -1Baniso -2Baniso -3
1-5.422 Å2-1.9532 Å2-2.0089 Å2
2--8.8038 Å28.4978 Å2
3----14.2258 Å2
Refine analyzeLuzzati coordinate error obs: 0.703 Å
Refinement stepCycle: LAST / Resolution: 3.3→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9277 0 91 8 9376
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00718621HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9433506HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5154SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes226HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2731HARMONIC5
X-RAY DIFFRACTIONt_it18621HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion3.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1275SEMIHARMONIC5
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_contact18756SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.42 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2712 156 5.2 %
Rwork0.2341 2845 -
all0.236 3001 -
obs--97.72 %
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)
12.5207-3.867-1.87863.56620.49810.0839-0.0917-0.0056-0.16240.46580.02330.33590.22040.03310.0683-0.0998-0.0439-0.0601-0.2951-0.01150.444-21.409317.3127-6.9104
26.6308-0.79532.21915.2126-1.72415.59520.0252-0.2067-0.18730.22780.1218-0.2175-0.2640.0099-0.1469-0.20280.0994-0.0159-0.2422-0.05610.602-7.21225.5952-0.2166
30.60685.6873-2.46057.2855-1.3319-0.312-0.08860.02550.0063-0.09340.09880.0356-0.00990.3061-0.0103-0.45290.32510.0179-0.2739-0.11990.5656-11.201320.6982-10.675
40.33591.044-0.69973.0273-2.05251.3860.0192-0.0463-0.02840.0624-0.042-0.0147-0.07840.01020.02280.09220.18850.18970.1352-0.06590.191-19.639821.88043.1895
58.5996-6.11660.04764.3996-1.00720.3239-0.11280.2191-0.05730.01030.10280.03170.2075-0.02940.01-0.24410.032-0.0542-0.4654-0.16520.5973-17.287816.6986-10.6145
62.4599-0.9738-0.47733.7277-0.23851.5881-0.4528-0.70340.20870.93050.3830.10350.49860.00570.06970.09050.26590.0543-0.0737-0.03970.186312.8386-13.57595.8816
72.05643.22690.31414.3572-0.6994-0.4012-0.2516-0.03310.147-0.29280.21720.4197-0.0041-0.07660.0344-0.13670.03420.0078-0.2621-0.07250.35488.0188-35.2173-16.5516
85.8845-4.2954-3.75932.4751-1.64518.0496-0.12780.26730.3366-0.64410.0913-0.19910.38430.19240.03650.0442-0.06060.125-0.2024-0.07540.359422.2587-23.5996-23.2177
91.83520.32053.342611.9721-2.23910.4481-0.0745-0.0698-0.2574-0.14760.2924-0.04270.04060.2305-0.2179-0.31460.06580.0686-0.1596-0.04550.249118.2712-38.6699-12.6264
10-0.0561-0.52480.16262.693-1.69411.19110.015-0.0160.0343-0.10320.0412-0.13790.0252-0.0037-0.05610.2343-0.168-0.05510.244-0.08540.0229.7792-39.8333-26.6376
1110.20855.83070.92413.46710.192-0.0513-0.0086-0.0499-0.08230.02740.03210.0483-0.1358-0.0243-0.0234-0.14040.05650.0743-0.4771-0.14960.49812.2036-34.7055-12.6759
124.28911.67812.29895.2467-0.22430.5504-0.42990.76640.0403-1.08850.51310.0591-0.40830.296-0.08320.0592-0.22340.0742-0.1868-0.09640.28942.3394-4.4343-29.3056
133.7108-0.1650.25222.66452.00982.5096-0.0956-0.0749-0.2150.11650.3027-0.2723-0.1952-0.1709-0.2071-0.2635-0.0121-0.0546-0.3895-0.06050.4255-24.9159-48.0855-1.1176
143.65095.43660.94783.2710.44066.94980.0267-0.0477-0.15620.1184-0.0737-0.0978-0.09910.42770.0470.05720.0087-0.03880.0441-0.12210.2086-16.7938-42.423317.7003
150.18793.94391.93365.90521.72964.05120.0077-0.18-0.03020.39210.1021-0.13680.1874-0.1334-0.1098-0.05750.21360.1044-0.02750.00620.1275-29.8799-52.94568.896
16-0.05233.8410.2063.4775-0.709-0.2033-0.0356-0.33370.05280.00030.0786-0.00360.0483-0.0225-0.0431-0.03260.1474-0.0392-0.27140.08410.3299-15.7872-54.92260.9685
171.4574-0.0147-1.2340.67820.2184-0.2686-0.0856-0.4022-0.05510.30070.16750.3326-0.00180.014-0.0819-0.01750.1023-0.0121-0.2229-0.04350.3931-28.157-47.58294.3956
180.62340.80981.62921.72480.54263.64040.0681-0.2981-0.24280.47970.0395-0.40170.21630.2897-0.10760.1554-0.1385-0.13250.2825-0.157-0.1597-3.535-32.735938.301
193.3630.6202-1.65974.1785-0.6533-0.4349-0.12690.0933-0.2609-0.21020.276-0.39720.3094-0.2327-0.1491-0.37810.04690.0237-0.4019-0.09050.46853.880729.9427-21.546
201.2659-2.6298-4.77442.57781.48319.7904-0.02650.40960.0674-0.69040.2244-0.0890.10940.3785-0.19790.176-0.1479-0.0039-0.0933-0.14770.14876.873429.7683-36.4289
212.18980.32591.9210.74091.92871.0109-0.27840.44390.0388-0.66620.32430.11260.04280.0083-0.046-0.0872-0.03560.0078-0.3792-0.0360.50371.201431.1671-23.5598
220.1571-1.7258-0.94641.76183.94875.05770.0636-0.18380.0979-0.15220.1649-0.3349-0.1587-0.1309-0.22850.3602-0.27440.16340.2981-0.3073-0.438121.100616.0621-66.6853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 6-44)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 45-72)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 73-96)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 97-102)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 103-165)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 166-921)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 6-44)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 45-72)
9X-RAY DIFFRACTION9(CHAIN B AND RESID73-96)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 97-102)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 103-165)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 166-921)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 8-44)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 45-72)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 73-96)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 97-102)
17X-RAY DIFFRACTION17(CHAIN C AND RESID103 - CAND RESID165)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 166-546)
19X-RAY DIFFRACTION19(CHAIN D AND RESID 8-41)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 42-97)
21X-RAY DIFFRACTION21(CHAIN D AND RESID 98-159)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 160-921)

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