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- PDB-5apd: Hen Egg White Lysozyme not illuminated with 0.4THz radiation -

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Entry
Database: PDB / ID: 5apd
TitleHen Egg White Lysozyme not illuminated with 0.4THz radiation
ComponentsLYSOZYME C
KeywordsHYDROLASE
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLundholm, I. / Rodilla, H. / Wahlgren, W.Y. / Duelli, A. / Bourenkov, G. / Vukusic, J. / Friedman, R. / Stake, J. / Schneider, T. / Katona, G.
CitationJournal: Struct.Dyn. / Year: 2015
Title: Terahertz Radiation Induces Non-Thermal Structural Changes Associated with Frohlich Condensation in a Protein Crystal
Authors: Lundholm, I. / Rodilla, H. / Wahlgren, W.Y. / Duelli, A. / Bourenkov, G. / Vukusic, J. / Friedman, R. / Stake, J. / Schneider, T. / Katona, G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 15, 2015 / Release: Jan 13, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 13, 2016Structure modelrepositoryInitial release
1.1Feb 3, 2016Structure modelDatabase references
1.2Mar 7, 2018Structure modelData collectiondiffrn_source_diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3542
Polyers14,3311
Non-polymers231
Water64936
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)79.350, 79.350, 37.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP 43 21 2

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Components

#1: Protein/peptide LYSOZYME C / 1 / 4-BETA-N-ACETYLMURAMIDASE C / ALLERGEN GAL D IV / HEN EGG WHITE LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1 / Source: (natural) GALLUS GALLUS (chicken) / Details: HEN EGG WHITE / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 38.6 %
Description: DATA WERE COLLECTED WITH EXTREME FINE SLICING AND ONLY EVERY SECOND IMAGE WAS USED
Crystal growpH: 4.5
Details: 50MM NA ACETATE, PH 4.5 1M NACL 25% ETHYLENE GLYCOL 30-100MG/ML HEWL IN 50MM NA ACETATE, PH 4.5

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.702949
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.702949 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 11829 / % possible obs: 90.9 % / Observed criterion σ(I): 2 / Redundancy: 197 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.1
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 10.1 / % possible all: 65.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→15 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.196-5 %
Rwork0.172--
obs-1365390.9 %
Refinement stepCycle: LAST / Resolution: 1.7→15 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms100001361037

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