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- PDB-6hu5: STRUCTURE OF HEWL BY ELECTRON DIFFRACTION AND MICROFOCUS DIFFRACTION -

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Basic information

Entry
Database: PDB / ID: 6hu5
TitleSTRUCTURE OF HEWL BY ELECTRON DIFFRACTION AND MICROFOCUS DIFFRACTION
ComponentsLysozyme C
KeywordsHYDROLASE / LYSOZYME / HEWL / ED / ELECTRON / DIFFRACTION / CRYSTAL / CHLORIDE / HALOGEN / PROTEIN / DIMER / MICROFOCUS
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 / cell wall macromolecule catabolic process / killing of cells of other organism / lysozyme / lysozyme activity / 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 / cryo EM / 2.8 Å resolution
AuthorsGarau, G.
CitationJournal: Iucrj / Year: 2019
Title: Nanobeam precession-assisted 3D electron diffraction reveals a new polymorph of hen egg-white lysozyme
Authors: Lanza, A. / Margheritis, E. / Mugnaioli, E. / Cappello, V. / Garau, G. / Gemmi, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 5, 2018 / Release: Jan 23, 2019

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Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7695
Polyers28,6622
Non-polymers1063
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)730
ΔGint (kcal/M)-17
Surface area (Å2)12750
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)31.849, 54.380, 71.788
Angle α, β, γ (deg.)90.00, 98.82, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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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.: 2 / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Formula: Cl / Chloride

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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: HWEL / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: NATURAL
Source (natural)Organism: Gallus gallus (chicken)
Buffer solutionpH: 7
Buffer componentConc.: 1.5 mg/mL / Name: Sodium Chloride / Formula: NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE
CrystalDensity Matthews: 2.07 / Density percent sol: 40.5 %
Crystal growDetails: 1.5 M SODIUM CHLORIDE

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Data collection

MicroscopyMicroscope model: ZEISS LIBRA120PLUS
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: OTHER
Electron lensMode: DARK FIELD
Image recordingElectron dose: 9 e/Å2 / Film or detector model: OTHER
EM diffractionCamera length: 800 mm
EM diffraction shellFourier space coverage: 67.1 / High resolution: 2.8 Å / Low resolution: 2.93 Å / Multiplicity: 2.8 / Number of structure factors: 2993 / Phase residual: 30 deg.
EM diffraction statsFourier space coverage: 90 / High resolution: 2.8 Å / Number of intensities measured: 10909 / Number of structure factors: 3905 / Overall phase error: 78 deg. / Overall phase residual: 30.5 deg. / Phase error rejection criteria: NULL / R merge: 0.655 / R sym: 0.655
DiffractionMean temperature: 1 kelvins
SourceSource: LaB6 THERMOIONIC SOURCE / Wavelength: 0.0335
DetectorType: ASI / Detector: OTHER / Collection date: Oct 1, 2018
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: electron
Radiation wavelengthWavelength: 0.0335 Å / Relative weight: 1
ReflectionD resolution high: 2.8 Å / D resolution low: 42.67 Å / Number obs: 3906 / Rmerge I obs: 0.655 / NetI over sigmaI: 1.6 / Redundancy: 2.8 % / Percent possible obs: 66.5
Reflection shellRmerge I obs: 0.839 / Highest resolution: 2.8 Å / Lowest resolution: 2.97 Å / MeanI over sigI obs: 0.8 / Redundancy: 2.8 % / Percent possible all: 67.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
XDSphasing
CCP4phasing
PHENIX(1.13_2998)refinement
EM software
IDNameVersionCategory
6PHENIX1.13model fitting
8PHENIX1.13molecular replacement
13PHENIX1.13model refinement
EM 3D crystal entityAngle alpha: 9 deg. / Angle beta: 98.82 deg. / Angle gamma: 9 deg. / Length a: 31.849 Å / Length b: 54.38 Å / Length c: 71.788 Å / Space group name: P 1 21 1 / Space group num: 4
CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingOverall b value: 10.8 / Ref protocol: OTHER / Target criteria: CORRELATION COEF
Atomic model buildingPDB-ID: 1B2K
RefineOverall SU ML: 0.51 / R Free selection details: RANDOM / Cross valid method: NONE / Sigma F: 1.34 / Overall phase error: 29.86
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Least-squares processR factor R free: 0.339 / R factor R work: 0.2975 / R factor obs: 0.2995 / Highest resolution: 2.8 Å / Lowest resolution: 42.67 Å / Number reflection R free: 177 / Number reflection obs: 3840 / Percent reflection R free: 4.61 / Percent reflection obs: 63.05
Refine hist #LASTHighest resolution: 2.801 Å / Lowest resolution: 31.473 Å
Number of atoms included #LASTProtein: 1980 / Nucleic acid: 0 / Ligand: 3 / Solvent: 0 / Total: 1983
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0042037
ELECTRON CRYSTALLOGRAPHYf_angle_d0.7762761
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d13.1801408
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.047286
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.004359
Refine LS shellHighest resolution: 2.801 Å / R factor R free: 0.339 / R factor R work: 0.2975 / Lowest resolution: 2.97 Å / Number reflection R free: 177 / Number reflection R work: 3663 / Percent reflection obs: 63
Refine TLS

Method: refined / Refine ID: ELECTRON CRYSTALLOGRAPHY

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.0278-0.00990.00170.19500.02430.17640.0165-0.0482-0.01250.0139-0.05400.05830.09320.0384-0.34860.00610.02500.0314-0.26180.0970-0.0176-3.4312-9.392626.2232
20.0711-0.0021-0.03130.0642-0.01850.0478-0.03010.0513-0.0465-0.0787-0.0250-0.1316-0.0610-0.0100-0.10190.02160.0256-0.05720.1761-0.11590.29038.1831-36.101812.3240
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1ELECTRON CRYSTALLOGRAPHY1(chain A and resseq 1:129)
2ELECTRON CRYSTALLOGRAPHY2(chain B and resseq 1:129)

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