[English] 日本語
Yorodumi
- PDB-1o72: Crystal structure of the water-soluble state of the pore-forming ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o72
TitleCrystal structure of the water-soluble state of the pore-forming cytolysin Sticholysin II complexed with phosphorylcholine
ComponentsSTICHOLYSIN II
KeywordsCYTOLYSIN / PORE-FORMING TOXIN / MEMBRANE INTERACTION / HEMOLYSIS
Function / homology
Function and homology information


nematocyst / pore complex assembly / cytolysis in another organism / other organism cell membrane / pore complex / monoatomic cation transport / channel activity / toxin activity / extracellular region / identical protein binding
Similarity search - Function
Sea anemone actinoporin-like / : / Sea anemone cytotoxic protein / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHOCHOLINE / DELTA-stichotoxin-She4b
Similarity search - Component
Biological speciesSTOICHACTIS HELIANTHUS (sea anemone)
MethodX-RAY DIFFRACTION / Resolution: 2.41 Å
AuthorsMancheno, J.M. / Martinez-Ripoll, M. / Gavilanes, J.G. / Hermoso, J.A.
CitationJournal: Structure / Year: 2003
Title: Crystal and Electron Microscopy Structures of Sticholysin II Actinoporin Reveal Insights Into the Mechanism of Membrane Pore Formation
Authors: Mancheno, J.M. / Martin-Benito, J. / Martinez-Ripoll, M. / Gavilanes, J.G. / Hermoso, J.A.
History
DepositionOct 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: STICHOLYSIN II
B: STICHOLYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9744
Polymers38,6062
Non-polymers3682
Water2,612145
1
A: STICHOLYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4872
Polymers19,3031
Non-polymers1841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: STICHOLYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4872
Polymers19,3031
Non-polymers1841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.630, 43.250, 119.520
Angle α, β, γ (deg.)90.00, 90.73, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein STICHOLYSIN II / CYTOLYSIN ST II / CYTOLYSIN III / CYTOTOXIN


Mass: 19302.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) STOICHACTIS HELIANTHUS (sea anemone) / References: UniProt: P07845
#2: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H15NO4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS CARDIAC STIMULATORY AND HEMOLYTIC PROTEIN IS A CHANNEL-FORMING AND/OR MEMBRANE-PENETRATING ...THIS CARDIAC STIMULATORY AND HEMOLYTIC PROTEIN IS A CHANNEL-FORMING AND/OR MEMBRANE-PENETRATING PROTEIN THAT FORMS ION CHANNELS. MEMBER OF THE TENEBROSIN FAMILY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.5
Details: 0.1M TRIS, PH 7.5, 0.2 M LITHIUM SULFATE, 30%(W/V) PEG 4000

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 26 Å2

-
Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
RefinementResolution: 2.41→14.94 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 873283.86 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 652 5.1 %RANDOM
Rwork0.212 ---
obs0.212 12768 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.7125 Å2 / ksol: 0.374912 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.35 Å20 Å21.67 Å2
2--3.2 Å20 Å2
3---2.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.41→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 22 145 2889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.41→2.56 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 109 5.6 %
Rwork0.279 1840 -
obs--89.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2POC_XPLOR_PAR.TXT
X-RAY DIFFRACTION3WATER_REP.PARAM

+
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