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- PDB-7y6a: Crystal structure of Chicken Egg Lysozyme -

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Basic information

Entry
Database: PDB / ID: 7y6a
TitleCrystal structure of Chicken Egg Lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / cell / enzyme
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDeMirci, H.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government118C270 Turkey
CitationJournal: Turk J Biol / Year: 2023
Title: Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source " Turkish DeLight ".
Authors: Atalay, N. / Akcan, E.K. / Gul, M. / Ayan, E. / Destan, E. / Ertem, F.B. / Tokay, N. / Cakilkaya, B. / Nergiz, Z. / Karakadioglu, G. / Kepceoglu, A. / Yapici, I. / Tosun, B. / Baldir, N. / ...Authors: Atalay, N. / Akcan, E.K. / Gul, M. / Ayan, E. / Destan, E. / Ertem, F.B. / Tokay, N. / Cakilkaya, B. / Nergiz, Z. / Karakadioglu, G. / Kepceoglu, A. / Yapici, I. / Tosun, B. / Baldir, N. / Yildirim, G. / Johnson, J.A. / Guven, O. / Shafiei, A. / Arslan, N.E. / Yilmaz, M. / Kulakman, C. / Paydos, S.S. / Cinal, Z.S. / Sabanoglu, K. / Pazarceviren, A. / Yilmaz, A. / Canbay, B. / Asci, B. / Kartal, E. / Tavli, S. / Caliseki, M. / Goc, G. / Mermer, A. / Yesilay, G. / Altuntas, S. / Tateishi, H. / Otsuka, M. / Fujita, M. / Tekin, S. / Ciftci, H. / Durdagi, S. / Dinler Doganay, G. / Karaca, E. / Kaplan Turkoz, B. / Kabasakal, B.V. / Kati, A. / Demirci, H.
History
DepositionJun 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3202
Polymers16,2581
Non-polymers621
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint1 kcal/mol
Surface area6540 Å2
Unit cell
Length a, b, c (Å)77.350, 77.350, 38.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

21A-425-

HOH

31A-433-

HOH

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Components

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


Mass: 16257.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 31.85 %
Crystal growTemperature: 294 K / Method: microbatch
Details: 0.09 M HEPES-NaOH pH 7.5, 1.26 M sodium citrate tribasic dihydrate, 10% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Feb 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→24.46 Å / Num. obs: 19182 / % possible obs: 98.9 % / Redundancy: 2 % / Rrim(I) all: 0.08 / Net I/σ(I): 15
Reflection shellResolution: 1.5→1.78 Å / Rrim(I) all: 0.328

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Processing

Software
NameVersionClassification
CrysalisProdata scaling
PHENIXdev_3318refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IJV

3ijv


Resolution: 1.5→24.46 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.1 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2559 679 3.54 %
Rwork0.2218 18503 -
obs0.2231 19182 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.44 Å2 / Biso mean: 18.9246 Å2 / Biso min: 3.03 Å2
Refinement stepCycle: final / Resolution: 1.5→24.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 0 134 1124
Biso mean---27.82 -
Num. residues----128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.61580.27521300.2275355797
1.6158-1.77840.27231330.2265360699
1.7784-2.03560.22691350.2206368999
2.0356-2.56420.27821360.22753721100
2.5642-24.460.24751450.21733930100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2144-0.14150.35292.31550.01332.55950.21540.28550.06570.0244-0.3737-0.3448-0.12290.14730.12210.1309-0.00520.03280.14940.07720.16587.7338-15.6604-8.5131
27.55152.81552.27018.64562.17381.0643-0.11880.04920.0050.1886-0.1721-0.5903-0.24250.42680.22050.0926-0.0114-0.01410.1420.08510.182512.1686-24.67382.3138
34.794-0.93241.18482.55320.23151.47290.01020.03140.01220.0432-0.0890.0250.0115-0.03720.07580.0978-0.00150.02150.10010.02390.09482.3462-24.2837-4.8834
41.98-0.7735-1.96621.5102-0.08897.2431-0.06490.1952-0.23710.0514-0.00140.27710.2005-0.40260.06190.10720.02370.0170.09560.03150.1831-9.322-17.2183-0.4406
53.7251-5.0997-2.70557.28733.48925.4303-0.1553-0.3782-0.10060.20370.2368-0.10210.30950.2642-0.05580.12090.02690.0110.09870.010.086-4.9191-16.8651.826
66.483-4.5452.55196.2235-0.9124.3374-0.3317-0.5503-0.11650.47170.23250.17750.2462-0.34880.05910.17910.01960.02750.17050.01480.1286-7.4504-15.179310.9399
76.1166-0.02980.47782.29860.50465.3592-0.1614-0.78980.02420.2850.0473-0.14560.0751-0.06820.07760.17840.0438-0.02140.18220.01340.1178-4.4903-13.508714.4594
82.4749-1.0602-2.47760.5111.18922.7480.01990.16120.37-0.1663-0.0364-0.1977-0.3226-0.01050.01120.18270.008-0.0080.13830.04220.2415-0.4802-8.80290.7119
97.50131.1442-1.77445.8818-3.60975.98430.0788-0.27220.14450.6118-0.1278-0.2565-0.29190.18320.04270.11950.0024-0.03380.1022-0.01380.10655.8225-17.00596.4225
109.2912-0.71061.77663.48050.71794.1837-0.0488-0.4288-0.05390.70610.14520.0673-0.1873-0.3002-0.08350.17470.02310.02140.10250.02050.09752.1733-27.43837.4799
116.2293-0.93533.04437.31831.81812.21540.1163-0.45120.11670.38-0.1220.24740.212-0.3757-0.00470.0706-0.01210.01270.1237-0.010.0952-2.5158-30.9131-0.7424
122.45471.7417-2.69293.4426-1.72014.6754-0.1552-0.0397-0.1155-0.3007-0.116-0.45770.41810.40940.26270.12820.04320.03470.11850.01810.12575.5951-31.7792-7.7154
139.22630.89111.19657.59042.25328.1769-0.15770.906-0.3189-0.9645-0.0171-0.68040.06330.4770.11450.19040.04560.09010.3324-0.03540.212811.2259-23.8195-15.2585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )A1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 24 )A16 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 36 )A25 - 36
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 50 )A37 - 50
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 58 )A51 - 58
6X-RAY DIFFRACTION6chain 'A' and (resid 59 through 68 )A59 - 68
7X-RAY DIFFRACTION7chain 'A' and (resid 69 through 78 )A69 - 78
8X-RAY DIFFRACTION8chain 'A' and (resid 79 through 88 )A79 - 88
9X-RAY DIFFRACTION9chain 'A' and (resid 89 through 100 )A89 - 100
10X-RAY DIFFRACTION10chain 'A' and (resid 101 through 108 )A101 - 108
11X-RAY DIFFRACTION11chain 'A' and (resid 109 through 114 )A109 - 114
12X-RAY DIFFRACTION12chain 'A' and (resid 115 through 123 )A115 - 123
13X-RAY DIFFRACTION13((chain 'A' and resid 124 through 128) or (chain 'A' and resid 201))A124 - 129

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