[English] 日本語
Yorodumi
- PDB-3eb7: Crystal Structure of Insecticidal Delta-Endotoxin Cry8Ea1 from Ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eb7
TitleCrystal Structure of Insecticidal Delta-Endotoxin Cry8Ea1 from Bacillus Thuringiensis at 2.2 Angstroms Resolution
ComponentsInsecticidal Delta-Endotoxin Cry8Ea1
KeywordsTOXIN / Endotoxin / Cry8E / Bacillus Thuringiensis
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
ACETATE ION / Crystaline entomocidal protoxin
Similarity search - Component
Biological speciesBacillus Thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGuo, S. / Ye, S. / Song, F. / Zhang, J. / Wei, L. / Shu, C.L.
CitationJournal: J.Struct.Biol. / Year: 2009
Title: Crystal structure of Bacillus thuringiensis Cry8Ea1: An insecticidal toxin toxic to underground pests, the larvae of Holotrichia parallela.
Authors: Guo, S. / Ye, S. / Liu, Y. / Wei, L. / Xue, J. / Wu, H. / Song, F. / Zhang, J. / Wu, X. / Huang, D. / Rao, Z.
History
DepositionAug 27, 2008Deposition site: RCSB / Processing site: PDBJ
SupersessionSep 16, 2008ID: 2QKG
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Insecticidal Delta-Endotoxin Cry8Ea1
B: Insecticidal Delta-Endotoxin Cry8Ea1
C: Insecticidal Delta-Endotoxin Cry8Ea1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,31219
Polymers198,8863
Non-polymers1,42616
Water19,8351101
1
A: Insecticidal Delta-Endotoxin Cry8Ea1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5464
Polymers66,2951
Non-polymers2513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Insecticidal Delta-Endotoxin Cry8Ea1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0279
Polymers66,2951
Non-polymers7318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Insecticidal Delta-Endotoxin Cry8Ea1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7396
Polymers66,2951
Non-polymers4435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
4
B: Insecticidal Delta-Endotoxin Cry8Ea1
hetero molecules

B: Insecticidal Delta-Endotoxin Cry8Ea1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,05418
Polymers132,5912
Non-polymers1,46316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5550 Å2
ΔGint-165 kcal/mol
Surface area43380 Å2
MethodPISA
5
A: Insecticidal Delta-Endotoxin Cry8Ea1
C: Insecticidal Delta-Endotoxin Cry8Ea1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,28510
Polymers132,5912
Non-polymers6948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-99 kcal/mol
Surface area42660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)407.282, 47.956, 103.121
Angle α, β, γ (deg.)90.00, 91.12, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Insecticidal Delta-Endotoxin Cry8Ea1


Mass: 66295.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus Thuringiensis (bacteria) / Strain: Bt185 / Gene: cry8Ea1 / Plasmid: pSTK / Production host: Bacillus Thuringiensis (bacteria) / Strain (production host): BtHD-73(Cry-) / References: UniProt: B3LEP7*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS NOT AVAILABLE IN UNIPROT DATABASE AT THE TIME OF PROCESSING.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.41 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2006 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→204.1 Å / Num. all: 101555 / Num. obs: 98915 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.07 / Num. unique all: 10105 / Rsym value: 0.46 / % possible all: 84.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CIY

1ciy


Resolution: 2.3→43.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.447 / SU ML: 0.158 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.349 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23009 8885 10 %RANDOM
Rwork0.16235 ---
all0.17103 80780 --
obs0.16913 79964 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.555 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å20.74 Å2
2--0.28 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14049 0 77 1101 15227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02214499
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.95219722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71651770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9123.657670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.285152354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9971591
X-RAY DIFFRACTIONr_chiral_restr0.1080.22157
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211078
X-RAY DIFFRACTIONr_nbd_refined0.2080.26799
X-RAY DIFFRACTIONr_nbtor_refined0.3090.29914
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.21055
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.2113
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.234
X-RAY DIFFRACTIONr_mcbond_it0.8561.58998
X-RAY DIFFRACTIONr_mcangle_it1.454214286
X-RAY DIFFRACTIONr_scbond_it2.39936330
X-RAY DIFFRACTIONr_scangle_it3.6594.55433
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 559 -
Rwork0.197 5524 -
obs--93.14 %

+
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