[English] 日本語
Yorodumi
- PDB-6owk: Crystal structure of a Bacillus thuringiensis Cry1B.867 tryptic c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6owk
TitleCrystal structure of a Bacillus thuringiensis Cry1B.867 tryptic core variant
ComponentsPesticidal crystal protein Cry1Be, Cry1K-like protein chimera
KeywordsTOXIN / Bacillus thuringiensis / Cry toxin / B.t.
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 Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / 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 Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / 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 Cry1Be / Pesticidal crystal protein Cry1Ka / Crystaline entomocidal protoxin
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.698 Å
AuthorsRydel, T.J. / Evdokimov, A. / Beishir, S.C.
CitationJournal: Appl.Environ.Microbiol. / Year: 2019
Title: Bacillus thuringiensis Cry1Da_7 and Cry1B.868 Protein Interactions with Novel Receptors Allow Control of Resistant Fall Armyworms, Spodoptera frugiperda (J.E. Smith).
Authors: Wang, Y. / Wang, J. / Fu, X. / Nageotte, J.R. / Silverman, J. / Bretsnyder, E.C. / Chen, D. / Rydel, T.J. / Bean, G.J. / Li, K.S. / Kraft, E. / Gowda, A. / Nance, A. / Moore, R.G. / Pleau, M. ...Authors: Wang, Y. / Wang, J. / Fu, X. / Nageotte, J.R. / Silverman, J. / Bretsnyder, E.C. / Chen, D. / Rydel, T.J. / Bean, G.J. / Li, K.S. / Kraft, E. / Gowda, A. / Nance, A. / Moore, R.G. / Pleau, M.J. / Milligan, J.S. / Anderson, H.M. / Asiimwe, P. / Evans, A. / Moar, W.J. / Martinelli, S. / Head, G.P. / Haas, J.A. / Baum, J.A. / Yang, F. / Kerns, D.L. / Jerga, A.
History
DepositionMay 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pesticidal crystal protein Cry1Be, Cry1K-like protein chimera


Theoretical massNumber of molelcules
Total (without water)69,7141
Polymers69,7141
Non-polymers00
Water0
1
A: Pesticidal crystal protein Cry1Be, Cry1K-like protein chimera

A: Pesticidal crystal protein Cry1Be, Cry1K-like protein chimera

A: Pesticidal crystal protein Cry1Be, Cry1K-like protein chimera


Theoretical massNumber of molelcules
Total (without water)209,1433
Polymers209,1433
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6550 Å2
ΔGint-4 kcal/mol
Surface area64350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.176, 106.176, 85.302
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Pesticidal crystal protein Cry1Be, Cry1K-like protein chimera / 139 kDa crystal protein / Crystaline entomocidal protoxin / Insecticidal delta-endotoxin CryIB(e)


Mass: 69714.469 Da / Num. of mol.: 1
Fragment: Cry1Be (UNP residues 35-510) + Cry1K (UNP residues 481-621)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: cry1Be, 158C2B, cryIB(e) / Production host: Bacillus thuringiensis (bacteria) / Variant (production host): 867
References: UniProt: O85805, UniProt: V9I1B1, UniProt: Q45715*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40 % / Description: Star of David-shaped, six-sided crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.3 / Details: 20% PEG3350, 0.2 M ammonium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 6, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.698→38.691 Å / Num. obs: 15172 / % possible obs: 93.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 25.2
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 4.83 / Num. unique obs: 597 / % possible all: 79.6

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EB7

3eb7


Resolution: 2.698→38.691 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.97
RfactorNum. reflection% reflectionSelection details
Rfree0.2769 1404 9.94 %Random selection
Rwork0.2228 ---
obs0.2284 14128 93.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.698→38.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 0 0 4664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044776
X-RAY DIFFRACTIONf_angle_d0.7686507
X-RAY DIFFRACTIONf_dihedral_angle_d4.9972812
X-RAY DIFFRACTIONf_chiral_restr0.046722
X-RAY DIFFRACTIONf_plane_restr0.006848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6979-2.79430.35361150.2991097X-RAY DIFFRACTION80
2.7943-2.90620.35621330.27491163X-RAY DIFFRACTION87
2.9062-3.03840.32121410.25671255X-RAY DIFFRACTION93
3.0384-3.19850.33761460.2581307X-RAY DIFFRACTION97
3.1985-3.39880.30191480.24291335X-RAY DIFFRACTION97
3.3988-3.6610.30911460.23871306X-RAY DIFFRACTION96
3.661-4.02910.28631490.22571318X-RAY DIFFRACTION97
4.0291-4.61130.24841390.19651309X-RAY DIFFRACTION95
4.6113-5.80660.23931420.19241324X-RAY DIFFRACTION96
5.8066-38.69530.22911450.19911310X-RAY DIFFRACTION93

+
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