[English] 日本語
Yorodumi
- PDB-5g37: MR structure of the binary mosquito larvicide BinAB at pH 5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g37
TitleMR structure of the binary mosquito larvicide BinAB at pH 5
Components
  • 41.9 KDA INSECTICIDAL TOXIN
  • LARVICIDAL TOXIN 51 KDA PROTEIN
KeywordsTOXIN / BINAB INSECTICIDAL TOXIN / PORE FORMING TOXIN / XFEL / SERIAL FEMTOSECOND CRYSTALLOGRAPHY / DE NOVO MIRAS PHASING / IN VIVO CRYSTALS
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / toxin activity
Similarity search - Function
Insecticidal crystal toxin / Insecticidal Crystal Toxin, P42 / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Binary larvicide subunit BinA / Binary larvicide subunit BinB
Similarity search - Component
Biological speciesLYSINIBACILLUS SPHAERICUS (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsColletier, J.P. / Sawaya, M.R. / Gingery, M. / Rodriguez, J.A. / Cascio, D. / Brewster, A.S. / Michels-Clark, T. / Boutet, S. / Williams, G.J. / Messerschmidt, M. ...Colletier, J.P. / Sawaya, M.R. / Gingery, M. / Rodriguez, J.A. / Cascio, D. / Brewster, A.S. / Michels-Clark, T. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / DePonte, D.P. / Sierra, R.G. / Laksmono, H. / Koglin, J.E. / Hunter, M.S. / W Park, H. / Uervirojnangkoorn, M. / Bideshi, D.L. / Brunger, A.T. / Federici, B.A. / Sauter, N.K. / Eisenberg, D.S.
CitationJournal: Nature / Year: 2016
Title: De Novo Phasing with X-Ray Laser Reveals Mosquito Larvicide Binab Structure.
Authors: Colletier, J. / Sawaya, M.R. / Gingery, M. / Rodriguez, J.A. / Cascio, D. / Brewster, A.S. / Michels-Clark, T. / Hice, R.H. / Coquelle, N. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / ...Authors: Colletier, J. / Sawaya, M.R. / Gingery, M. / Rodriguez, J.A. / Cascio, D. / Brewster, A.S. / Michels-Clark, T. / Hice, R.H. / Coquelle, N. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / Deponte, D.P. / Sierra, R.G. / Laksmono, H. / Koglin, J.E. / Hunter, M.S. / Park, H. / Uervirojnangkoorn, M. / Bideshi, D.K. / Brunger, A.T. / Federici, B.A. / Sauter, N.K. / Eisenberg, D.S.
History
DepositionApr 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3Nov 15, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 1.4Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.5Aug 28, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.pdbx_CC_half
Revision 1.6Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
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: 41.9 KDA INSECTICIDAL TOXIN
B: LARVICIDAL TOXIN 51 KDA PROTEIN


Theoretical massNumber of molelcules
Total (without water)92,9702
Polymers92,9702
Non-polymers00
Water12,935718
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-12.2 kcal/mol
Surface area33980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.787, 96.996, 127.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 41.9 KDA INSECTICIDAL TOXIN / STRAINS 1593/2362/2317.3 / TOXIC COMPONENT OF BINARY TOXIN BINAB


Mass: 41483.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LYSINIBACILLUS SPHAERICUS (bacteria) / Strain: 2362 / Plasmid: BTI4Q7-PPHSP-1
Production host: BACILLUS THURINGIENSIS SEROVAR ISRAELENSIS (bacteria)
Strain (production host): 4Q7 / References: UniProt: P06575
#2: Protein LARVICIDAL TOXIN 51 KDA PROTEIN / STRAINS 1593/2362 / RECEPTOR BINDING COMPONENT OF BINARY TOX IN BINAB


Mass: 51486.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LYSINIBACILLUS SPHAERICUS (bacteria) / Strain: 2362 / Description: NATURALLY OCCURRING NANO-CRYSTALS / Plasmid: BTI4Q7-PPHSP-1
Production host: BACILLUS THURINGIENSIS SEROVAR ISRAELENSIS (bacteria)
Strain (production host): 4Q7 / References: UniProt: P10565
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 718 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsONLY RESIDUES 3-366 ARE DEFINED IN THE ELECTRON DENSITY ONLY RESIDUES 29-448 ARE DEFINED IN THE ...ONLY RESIDUES 3-366 ARE DEFINED IN THE ELECTRON DENSITY ONLY RESIDUES 29-448 ARE DEFINED IN THE ELECTRON DENSITY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.4 % / Description: NONE
Crystal growpH: 5
Details: NATURALLY OCCURRING NANOCRYSTALS FORMED IN VIVO, pH 5

-
Data collection

DiffractionMean temperature: 287 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.459 / Wavelength: 1.459 Å
DetectorType: CORNELL-SLAC / Detector: PIXEL / Date: Feb 13, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.5→45 Å / Num. obs: 5495157 / % possible obs: 99.9 % / Observed criterion σ(I): 2.45 / Redundancy: 76.62 % / Biso Wilson estimate: 28.41 Å2 / CC1/2: 0.868 / Net I/σ(I): 6.34
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 8.61 % / Mean I/σ(I) obs: 2.46 / CC1/2: 0.28 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
cctbx.xfeldata reduction
cctbx.primedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FOY

5foy


Resolution: 2.5→24.643 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 1813 5 %
Rwork0.2111 --
obs0.2137 36193 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.23 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6322 0 0 718 7040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026636
X-RAY DIFFRACTIONf_angle_d0.4489046
X-RAY DIFFRACTIONf_dihedral_angle_d15.3353996
X-RAY DIFFRACTIONf_chiral_restr0.042986
X-RAY DIFFRACTIONf_plane_restr0.0031189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56760.42711310.35722426X-RAY DIFFRACTION89
2.5676-2.6430.40571300.33122475X-RAY DIFFRACTION91
2.643-2.72820.42641340.31062492X-RAY DIFFRACTION92
2.7282-2.82560.3821350.30172537X-RAY DIFFRACTION94
2.8256-2.93860.3331370.27692585X-RAY DIFFRACTION94
2.9386-3.07210.31291370.2492629X-RAY DIFFRACTION97
3.0721-3.23370.2931390.2342650X-RAY DIFFRACTION97
3.2337-3.43580.27011400.2092686X-RAY DIFFRACTION98
3.4358-3.70030.25531400.17962694X-RAY DIFFRACTION98
3.7003-4.07110.2131460.16962746X-RAY DIFFRACTION99
4.0711-4.65680.19971440.14782755X-RAY DIFFRACTION99
4.6568-5.85410.1841460.15722788X-RAY DIFFRACTION99
5.8541-24.6440.19931540.18182917X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 37.8554 Å / Origin y: 37.721 Å / Origin z: 13.4776 Å
111213212223313233
T0.2912 Å20.0195 Å2-0.0057 Å2-0.2935 Å20.0003 Å2--0.2872 Å2
L0.2209 °20.1415 °20.0434 °2-0.437 °20.1279 °2--0.2866 °2
S0.0056 Å °0.0151 Å °0.006 Å °-0.0017 Å °0.0102 Å °-0.0113 Å °-0.0405 Å °0.0092 Å °0 Å °
Refinement TLS groupSelection details: ALL

+
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