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Crystal structure of the chitinase Chi1 fitted into the 3D structure of the Yersinia entomophaga toxin complex

by single particle reconstruction, at 17 A resolution

Movie

Orientation:

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1978, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1978, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4a5q
TitleCrystal structure of the chitinase Chi1 fitted into the 3D structure of the Yersinia entomophaga toxin complex
DescriptorCHI1 (E.C.3.2.1.14)
KeywordsHYDROLASE, BACTERIAL TOXIN, INSECTICIDE
AuthorsBusby, J.N., Landsberg, M.J., Simpson, R.M., Jones, S.A., Hankamer, B., Hurst, M.R.H., Lott, J.S.
DateDeposition: 2011-10-27, Release: 2011-11-16
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1978, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1978, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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Article
Citation - primary
ArticleJ. Mol. Biol., Vol. 415, Issue 2, Page 359-71, Year 2012
TitleStructural analysis of Chi1 Chitinase from Yen-Tc: the multisubunit insecticidal ABC toxin complex of Yersinia entomophaga.
AuthorsJason N Busby, Michael J Landsberg, Robert M Simpson, Sandra A Jones, Ben Hankamer, Mark R H Hurst, J Shaun Lott
AgResearch Structural Biology Laboratory, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
KeywordsBacterial Toxins (chemistry), Chitin (metabolism, 1398-61-4), Chitinase (chemistry, 3.2.1.14), Cryoelectron Microscopy, Crystallography, X-Ray, Models, Molecular, New Zealand, Photorhabdus (genetics), Protein Structure, Quaternary, Soil Microbiology, Xenorhabdus (genetics), Yersinia (chemistry)
LinksPII: S0022-2836(11)01237-X, DOI: 10.1016/j.jmb.2011.11.018, PubMed: 22108167
Components
ID 1 : CHI1
Image
DescriptionCHI1
Typepolypeptide(L)
Formula weight60727.066 Da
Number of molecules5
ID1
Ec3.2.1.14
SourceMethod: Isolated from a genetically manipulated source
Gene: MH96\:\:9, ID:935293, YERSINIA ENTOMOPHAGA
Host: ID:469008, ESCHERICHIA COLI

, BL21(DE3), ROSETTA2, PDEST17, PLASMID
LinksUniProt: B6A876, Sequence view
Sample
Assembly
Aggregation statePARTICLE
DetailsPARTICLES WERE SELECTED USING SEMI-AUTOMATED PARTICLE SELECTION ( SWARMPS, E2BOXER.PY)
NameINSECTICIDAL TC FROM YERSINIA ENTOMOPHAGA STRAIN MH96 (DELETION CONSTRUCT 9)(AKA YEN-TC K9)
Buffer
Name25 MM TRIS, 130 MM NACL
Experiment
Reconstruction methodSINGLE PARTICLE
Sample preparation
pH7.5
Sample concentration0.1 mg/ml
Sample support
DetailsOTHER
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F30
Date2009-06-02
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose80 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationNominal: 59000 X
CsNominal: 2.0 mm
Nominal defocusMax: 950 nm, Min: 900 nm
Specimen holder
Temperature295 Kelvin
Detector
TypeGATAN USC 4000 (MODEL 895)
Image scans
Number digital images300
Processing
2D projection selection
Number of particles10604
Software nameXMIPP, EMAN
3D reconstruction
DetailsSUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1978.(DEPOSITION ID: 10324).
MethodCROSS-COMMON LINES, PROJECTION MATCHING
Resolution17 A
3D fitting
MethodRIGID BODY
Temperature factor22.09
Refinement ProtocolX-RAY
Refinement SpaceREAL
Target criteriaCROSS-CORRELATION COEFFICIENT
3D fitting list
3D Fitting ID1
PDB entry ID3OA5
Refine
Refine idELECTRON MICROSCOPY
Ls d res high17.00 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high17.00
Total atoms20005
Protein atoms20005
Download
PDB format
Allpdb4a5q.ent.gz
pdb4a5q.ent (uncompressed file)
Header onlypdb4a5q.ent.gz
mmCIF format
mmCIF4a5q.cif.gz
XML format
All4a5q.xml.gz
No-atom4a5q-noatom.xml.gz
Ext-atom4a5q-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 3.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.4 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.8 MB