[English] 日本語
Yorodumi
- PDB-1ji6: CRYSTAL STRUCTURE OF THE INSECTICIDAL BACTERIAL DEL ENDOTOXIN CRY... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ji6
TitleCRYSTAL STRUCTURE OF THE INSECTICIDAL BACTERIAL DEL ENDOTOXIN CRY3Bb1 BACILLUS THURINGIENSIS
ComponentsPESTICIDIAL CRYSTAL PROTEIN CRY3BB
KeywordsTOXIN / Cry3Bb1
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / : / toxin activity / signaling receptor binding
Similarity search - Function
Pesticidal crystal protein, central domain / Pesticidal crystal protein, N-terminal domain / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, central domain superfamily / Pesticidal crystal protein, C-terminal / delta endotoxin / Pesticidal crystal protein / Pesticidal crystal protein, N-terminal / Pesticidal crystal protein, N-terminal domain superfamily ...Pesticidal crystal protein, central domain / Pesticidal crystal protein, N-terminal domain / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, central domain superfamily / Pesticidal crystal protein, C-terminal / delta endotoxin / Pesticidal crystal protein / Pesticidal crystal protein, N-terminal / Pesticidal crystal protein, N-terminal domain superfamily / delta endotoxin, N-terminal domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Delta-Endotoxin; domain 1 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Pesticidal crystal protein Cry3Bb
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 2.4 Å
AuthorsCody, V.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of the insecticidal bacterial delta-endotoxin Cry3Bb1 of Bacillus thuringiensis.
Authors: Galitsky, N. / Cody, V. / Wojtczak, A. / Ghosh, D. / Luft, J.R. / Pangborn, W. / English, L.
#1: Journal: Nature / Year: 1991
Title: Crystal Structure of Insecticidal Delta-Endotoxin from Bacillus Thuringiensis at 2.5 Angstroms Resolution
Authors: Li, J. / Carroll, J. / Ellar, D.J.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: X-Ray Analysis of the Crystalline Parasporal Inclusion in Bacillus Thuringiensis Var. Tenebrionis
Authors: Li, J. / Henderson, R. / Carroll, J. / Ellar, D.
History
DepositionJun 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PESTICIDIAL CRYSTAL PROTEIN CRY3BB


Theoretical massNumber of molelcules
Total (without water)67,2061
Polymers67,2061
Non-polymers00
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.440, 131.810, 105.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein PESTICIDIAL CRYSTAL PROTEIN CRY3BB / INSECTICIDAL DELTA-ENDOTOXIN CRYIIIB(B) / CRYSTALLINE ENTOMOCIDAL PROTOXIN


Mass: 67206.133 Da / Num. of mol.: 1 / Fragment: Residues 64-652
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: EG7321 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06117
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCRY3Bb1 BELONGS TO THE "CRY" FAMILY OF DELTA-ENDOTOXINS, WHICH ARE PORE-FORMING INSECTICIDAL ...CRY3Bb1 BELONGS TO THE "CRY" FAMILY OF DELTA-ENDOTOXINS, WHICH ARE PORE-FORMING INSECTICIDAL PROTEIN TOXINS CONTAINED IN THE CRYSTALLINE PARASPORAL INCLUSIONS OF BACILLUS THURINGIENSIS. THE SUBCLASS III IS TOXIC SPECIFICALLY TO COLEOPTERAN INSECTS, I.E., BEETLES. THEY FUNCTION BY BINDING TO MIDGUT EPITHELIAL CELLS AND INDUCE COLLOIDOSMOTIC LYSIS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4 M NaBr, 0.1 M HEPES, 0.5% Lubrol PX, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: microdialysis
Details: Cody, V., (1992) Proteins Struct. Funct. Genet., 14. 324.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 M1dropNaBr
20.1 MHEPES1drop
30.5 %(w/v)Lubrol PX1drop
40.6 M1reservoirNaBr
50.1 MHEPES1reservoir
60.5 %(w/v)Lubrol PX1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 15, 1991
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→8 Å / Num. all: 91281 / Num. obs: 30077 / % possible obs: 72.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 30.22 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.02 / Net I/σ(I): 10.3
Reflection shellResolution: 2.4→8 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 6.8 / Num. unique all: 30077 / % possible all: 72.2
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 91281 / Rmerge(I) obs: 0.0766

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.4→8 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3049 -Random
Rwork0.175 ---
all0.185 30077 --
obs0.175 27379 72.2 %-
Displacement parametersBiso mean: 25.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4750 0 0 251 5001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.06
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.251
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.06
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.251

+
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