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- PDB-4a5q: Crystal structure of the chitinase Chi1 fitted into the 3D struct... -

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Basic information

Entry
Database: PDB / ID: 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
Specimen sourceYersinia entomophaga / bacteria
MethodElectron microscopy (17 Å resolution / Particle / Single particle)
AuthorsBusby, J.N. / Landsberg, M.J. / Simpson, R.M. / Jones, S.A. / Hankamer, B. / Hurst, M.R.H. / Lott, J.S.
CitationJ. Mol. Biol., 2012, 415, 359-371

J. Mol. Biol., 2012, 415, 359-371 Yorodumi Papers
Structural analysis of Chi1 Chitinase from Yen-Tc: the multisubunit insecticidal ABC toxin complex of Yersinia entomophaga.
Jason N Busby / Michael J Landsberg / Robert M Simpson / Sandra A Jones / Ben Hankamer / Mark R H Hurst / J Shaun Lott

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 27, 2011 / Release: Nov 16, 2011
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 16, 2011Structure modelrepositoryInitial release
1.1Jan 25, 2012Structure modelOther
1.2Sep 25, 2013Structure modelSource and taxonomy
1.3Aug 23, 2017Structure modelData collection / Refinement descriptionem_3d_fitting / em_software_em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Assembly

Deposited unit
A: CHI1
B: CHI1
C: CHI1
D: CHI1
E: CHI1


Theoretical massNumber of molelcules
Total (without water)303,6325
Polyers303,6325
Non-polymers00
Water0
#1
A: CHI1


Theoretical massNumber of molelcules
Total (without water)60,7261
Polyers60,7261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
#2
B: CHI1


Theoretical massNumber of molelcules
Total (without water)60,7261
Polyers60,7261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
#3
C: CHI1


Theoretical massNumber of molelcules
Total (without water)60,7261
Polyers60,7261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
#4
D: CHI1


Theoretical massNumber of molelcules
Total (without water)60,7261
Polyers60,7261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
#5
E: CHI1


Theoretical massNumber of molelcules
Total (without water)60,7261
Polyers60,7261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)
CHI1


Mass: 60726.355 Da / Num. of mol.: 5 / Source: (gene. exp.) Yersinia entomophaga / bacteria / References: UniProt: B6A876, EC: 3.2.1.14

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: INSECTICIDAL TC FROM YERSINIA ENTOMOPHAGA STRAIN MH96 (DELETION CONSTRUCT 9)(AKA YEN-TC K9)
Type: COMPLEX
Details: PARTICLES WERE SELECTED USING SEMI-AUTOMATED PARTICLE SELECTION ( SWARMPS, E2BOXER.PY)
Buffer solutionName: 25 MM TRIS, 130 MM NACL / Details: 25 MM TRIS, 130 MM NACL / pH: 7.5
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: uranyl formate
Specimen supportDetails: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30 / Date: Jun 2, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 / Nominal defocus max: 950 nm / Nominal defocus min: 900 nm / Cs: 2 mm
Specimen holderTemperature: 295 kelvins
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNumber digital images: 300
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryFitting IDImage processing ID
1SitusMODEL FITTING1
2EMANRECONSTRUCTION1
3XmippRECONSTRUCTION1
SymmetryPoint symmetry: C5
3D reconstructionMethod: CROSS-COMMON LINES, PROJECTION MATCHING / Resolution: 17 Å / Number of particles: 10604
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1978.(DEPOSITION ID: 10324).
Symmetry type: POINT
Atomic model buildingDetails: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY / Overall b value: 22.09 / Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 3OA5
Least-squares processHighest resolution: 17 Å
Refine hist #LASTHighest resolution: 17 Å
Number of atoms included #LASTProtein: 20005 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 20005

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