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- PDB-6h3b: Lysozyme: Machining protein microcrystals for structure determina... -

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Basic information

Entry
Database: PDB / ID: 6h3b
TitleLysozyme: Machining protein microcrystals for structure determination by electron diffraction
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / hydrolase
Function / homologyLysozyme-like domain superfamily / Lysozyme C / Glycoside hydrolase, family 22, conserved site / Glycoside hydrolase, family 22 / Glycoside hydrolase, family 22, lysozyme / C-type lysozyme/alpha-lactalbumin family / Alpha-lactalbumin / lysozyme C signature. / Neutrophil degranulation / Alpha-lactalbumin / lysozyme C family profile. / Antimicrobial peptides ...Lysozyme-like domain superfamily / Lysozyme C / Glycoside hydrolase, family 22, conserved site / Glycoside hydrolase, family 22 / Glycoside hydrolase, family 22, lysozyme / C-type lysozyme/alpha-lactalbumin family / Alpha-lactalbumin / lysozyme C signature. / Neutrophil degranulation / Alpha-lactalbumin / lysozyme C family profile. / Antimicrobial peptides / catabolism by organism of cell wall peptidoglycan in other organism / beta-N-acetylglucosaminidase activity / killing of cells of other organism / lysozyme / lysozyme activity / cell wall macromolecule catabolic process / cytolysis / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm / Lysozyme C
Function and homology information
Specimen sourceGallus gallus (chicken)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / 1.9 Å resolution
AuthorsDuyvesteyn, H.M.E. / Ginn, H.M. / Stuart, D.I.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Machining protein microcrystals for structure determination by electron diffraction.
Authors: Helen M E Duyvesteyn / Abhay Kotecha / Helen M Ginn / Corey W Hecksel / Emma V Beale / Felix de Haas / Gwyndaf Evans / Peijun Zhang / Wah Chiu / David I Stuart
Abstract: We demonstrate that ion-beam milling of frozen, hydrated protein crystals to thin lamella preserves the crystal lattice to near-atomic resolution. This provides a vehicle for protein structure ...We demonstrate that ion-beam milling of frozen, hydrated protein crystals to thin lamella preserves the crystal lattice to near-atomic resolution. This provides a vehicle for protein structure determination, bridging the crystal size gap between the nanometer scale of conventional electron diffraction and micron scale of synchrotron microfocus beamlines. The demonstration that atomic information can be retained suggests that milling could provide such detail on sections cut from vitrified cells.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 18, 2018 / Release: Sep 12, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 12, 2018Structure modelrepositoryInitial release
1.1Sep 26, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3672
Polyers14,3311
Non-polymers351
Water25214
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)80
ΔGint (kcal/M)-5
Surface area (Å2)6740
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)79.900, 79.900, 38.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP 43 21 2
Space group name HallP 4nw 2abw

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Components

#1: Protein/peptide Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Formula: Cl / Chloride
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / Reconstruction method: electron crystallography

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Sample preparation

ComponentName: lysozyme / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Gallus gallus (chicken)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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Data collection

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TALOS ARCTICA
Electron gunIllumination mode: OTHER
Electron lensMode: DIFFRACTION

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Processing

RefineR Free selection details: Copied from 5wr9.pdb / Cross valid method: FREE R-VALUE
Least-squares processR factor R free: 0.283 / R factor R work: 0.291 / Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Number reflection R free: 313 / Number reflection obs: 3508 / Percent reflection R free: 5 / Percent reflection obs: 38.67
Refine LS restraintsType: Rigid body
Refine LS shellHighest resolution: 1.9 Å / R factor R free: 0.729 / R factor R work: 0.532 / Lowest resolution: 2.14 Å / Number reflection R free: 10 / Number reflection R work: 307 / Percent reflection obs: 10.47

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