[English] 日本語
Yorodumi
- PDB-3zxg: lysenin sphingomyelin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zxg
Titlelysenin sphingomyelin complex
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: 3.12 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 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Derived calculations
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Dec 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LYSENIN
B: LYSENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5186
Polymers69,6922
Non-polymers8264
Water905
1
A: LYSENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5764
Polymers34,8461
Non-polymers7303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9422
Polymers34,8461
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)211.150, 37.200, 96.740
Angle α, β, γ (deg.)90.00, 104.03, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8497, 0.31144, 0.42592), (0.37571, -0.92379, -0.07383), (0.37047, 0.22274, -0.90174)
Vector: -1.84641, -15.3269, 53.19016)

-
Components

#1: Protein LYSENIN / EFL1


Mass: 34846.051 Da / Num. of mol.: 2
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-0SM / TRIMETHYL-[2-[[(2S,3S)-2-(OCTADECANOYLAMINO)-3-OXIDANYL-BUTOXY]-OXIDANYL-PHOSPHORYL]OXYETHYL]AZANIUM / N-OCTADECANOYL-D-ERYTHRO-SPHINGOSYLPHOSPHORYLCHOLINE


Mass: 537.733 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H58N2O6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBRAIN SPHINGOMYELIN IS REPRESENTED BY N-OCTADECANOYL-D-ERYTHRO- SPHINGOSYLPHOSPHORYLCHOLINE ...BRAIN SPHINGOMYELIN IS REPRESENTED BY N-OCTADECANOYL-D-ERYTHRO- SPHINGOSYLPHOSPHORYLCHOLINE (TRIMETHYL-[2-[[(2S,3S)-2-(OCTA DECANOYLAMINO)-3-OXIDANYL-BUTOXY]-OXIDANYL-PHOSPHORYL] OXYETHYL]AZANIUM - RESIDUE 0SM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.6 % / Description: NONE
Crystal growpH: 5.5 / Details: 0.1 M BIS-TRIS PH 5.5, 0.2 M LI2SO4.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.1→62.1 Å / Num. obs: 13456 / % possible obs: 99.7 % / Observed criterion σ(I): 6 / Redundancy: 7.2 % / Biso Wilson estimate: 82.75 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.3
Reflection shellResolution: 3.1→3.3 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.3 / % possible all: 99.6

-
Processing

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

3zx7


Resolution: 3.12→50.38 Å / Cor.coef. Fo:Fc: 0.8355 / Cor.coef. Fo:Fc free: 0.8177 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.488
Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. USED OPTION TO RESTRAIN IMPROPER TORSION AROUND CHIRAL CENTRES AROUND CHIRAL CENTRES FROM THE ...Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. USED OPTION TO RESTRAIN IMPROPER TORSION AROUND CHIRAL CENTRES AROUND CHIRAL CENTRES FROM THE EQUILIBRIUM TO GET BETTER MOLPROBITY CB DEVIATION SCORE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2707 665 4.94 %RANDOM
Rwork0.2387 ---
obs0.2404 13453 99.76 %-
Displacement parametersBiso mean: 99.13 Å2
Baniso -1Baniso -2Baniso -3
1-24.7865 Å20 Å218.1193 Å2
2---25.0078 Å20 Å2
3---0.2213 Å2
Refine analyzeLuzzati coordinate error obs: 0.8 Å
Refinement stepCycle: LAST / Resolution: 3.12→50.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4657 0 51 5 4713
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0079355HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9416823HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2587SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1361HARMONIC5
X-RAY DIFFRACTIONt_it9355HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion2.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion642SEMIHARMONIC5
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_contact9563SEMIHARMONIC4
LS refinement shellResolution: 3.12→3.37 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2812 133 4.9 %
Rwork0.2438 2579 -
all0.2456 2712 -
obs--99.76 %
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)
14.46073.2839-6.69891.7462-4.335-2.51560.1277-0.2402-0.06620.02370.3393-0.1780.6648-0.254-0.46690.0856-0.3954-0.26210.25990.2372-0.0479-0.862-20.20411.2956
2-0.87391.13511.38640-4.325710.14840.0537-0.0055-0.1281-0.1177-0.04950.0935-0.0104-0.2311-0.00430.3746-0.5353-0.35090.55530.2613-0.1148-10.2537-40.449819.4663
39.64882.1953-5.66535.8655-4.31136.949-0.0144-1.08730.2795-0.6586-0.0442-0.68740.9993-0.07110.0585-0.1946-0.1141-0.0020.0474-0.0215-0.208412.9707-17.63829.8389
40.40746.9184-0.91850.83433.60073.709-0.0918-0.45340.59580.0820.18260.14590.0623-0.6591-0.0908-0.3051-0.237-0.05750.46160.0887-0.3828-1.9261-18.36217.6499
5-0.3677-1.0692-0.5294.8069-7.896510.17650.1008-0.2597-0.15570.0999-0.1818-0.279-0.09720.10880.0811-0.0466-0.4621-0.51850.67370.350.4782-16.3122-36.73819.2384
69.04893.6089-3.08064.054-1.85872.33690.2291-0.36110.1711-0.35650.20240.03270.2695-0.9118-0.43150.0333-0.291-0.21130.51890.1921-0.234-4.2712-20.043311.6845
73.10320.1225-0.40190.4013-0.18390.50580.09450.11070.5629-0.00450.05210.05870.1294-0.1752-0.14670.0653-0.03510.0059-0.15860.0960.192836.5867-6.31891.9583
8-1.57420.31512.18630.8613-1.55587.8220.0459-0.113-0.08450.38850.06220.3910.2425-0.2091-0.1082-0.1716-0.3273-0.04320.74430.3837-0.5979-2.47490.780439.2128
98.9932-5.36457.14114.2913-3.035610.68530.0921-0.9803-0.11380.8624-0.10310.31180.0223-0.39140.0111-0.2854-0.5465-0.00420.78020.3232-0.6738-3.32925.755634.2726
106.04332.8715-8.66470.4631-4.58534.3115-0.0271-0.3553-0.05220.36030.06750.77990.04240.0859-0.0404-0.5891-0.3264-0.12830.90570.3884-0.4809-9.7794.199233.4524
111.64595.0555-4.37034.22211.48748.62420.0085-0.05510.14630.19780.10980.3073-0.0411-0.0066-0.11830.2114-0.5067-0.2860.48460.3423-0.4778-4.7337-5.393238.4457
1211.22742.75026.74874.62790.59658.7697-0.27481.49560.4649-0.34280.81780.23310.41680.7297-0.5431-0.0820.0498-0.08020.08430.1724-0.406328.81193.742364.0169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5-30)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 31-40)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 41-73)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 74-102)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 103-112)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 113-160)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 161-943)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 6-28)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 29-114)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 115-141)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 142-157)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 158-898)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more