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- PDB-8ya4: Crystal structure of a lysozyme form hen egg white -

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Basic information

Entry
Database: PDB / ID: 8ya4
TitleCrystal structure of a lysozyme form hen egg white
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme / egg white / crystal
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, C.Y. / Xu, Q. / Wang, W.W. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
Other government21ZR1471800 China
CitationJournal: To Be Published
Title: Crystallographic data collection using a multilayer monochromator on an undulator beamline at SSRF
Authors: Zhang, C.Y. / Xu, Q. / Wang, W.W. / Liang, M. / Yu, L. / Li, M.J. / Zhu, Z.M. / Huang, L.Q. / Li, Q.H. / Yu, F. / Wang, Y.Z. / Zhou, H. / Wang, Q.S.
History
DepositionFeb 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.819, 78.819, 37.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-239-

HOH

21A-252-

HOH

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Components

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


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate, 6% sodium chloride

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.924 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.924 Å / Relative weight: 1
ReflectionResolution: 2.1→39.41 Å / Num. obs: 7407 / % possible obs: 100 % / Redundancy: 24.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.291 / Rpim(I) all: 0.059 / Rrim(I) all: 0.297 / Χ2: 0.99 / Net I/σ(I): 20.2 / Num. measured all: 183398
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 100 % / Redundancy: 24.8 % / Rmerge(I) obs: 1.236 / Num. measured all: 14482 / Num. unique obs: 585 / CC1/2: 0.929 / Rpim(I) all: 0.252 / Rrim(I) all: 1.262 / Χ2: 1.09 / Net I/σ(I) obs: 6.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39.41 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 738 10.01 %
Rwork0.189 --
obs0.1939 7376 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 56 1057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071021
X-RAY DIFFRACTIONf_angle_d0.9651381
X-RAY DIFFRACTIONf_dihedral_angle_d7.487143
X-RAY DIFFRACTIONf_chiral_restr0.054144
X-RAY DIFFRACTIONf_plane_restr0.008181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.260.30111430.22051285X-RAY DIFFRACTION100
2.26-2.480.25181440.19611296X-RAY DIFFRACTION100
2.48-2.840.23931450.21531305X-RAY DIFFRACTION100
2.84-3.580.2161480.18891331X-RAY DIFFRACTION100
3.58-39.410.23351580.16691421X-RAY DIFFRACTION100
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)
12.51961.2216-0.50951.3976-1.90643.97710.08230.1273-0.4015-0.3595-0.0375-0.4538-0.0350.77340.04970.2409-0.01340.07290.188-0.07860.2406-16.3967-6.6001-18.8568
25.00570.01190.82941.24780.73370.60180.0737-0.2677-0.90780.7781-0.07840.37290.54050.2748-0.04270.27310.08680.04690.16510.04010.2683-23.7827-11.6387-7.9418
31.35581.2238-0.13421.24460.02450.9291-0.0424-0.02010.1734-0.0577-0.08110.112-0.1607-0.01640.01440.15-0.0099-0.01170.1641-0.01070.165-20.42384.9735-11.2873
42.81771.18290.71654.2452-0.81740.64880.3719-0.29040.670.7846-0.3706-0.0302-0.4675-0.37320.03210.3167-0.05730.03860.3005-0.0340.161-16.31218.05861.3093
50.8109-0.16220.26046.26291.21970.36820.229-0.7329-0.2690.97170.0805-0.02030.07780.1694-0.26690.3977-0.12590.03420.3345-0.00650.2439-14.36815.01724.7195
62.80010.980.85922.19560.17751.19230.1848-0.0061-0.16050.1177-0.06390.0228-0.05720.058-0.0830.1688-0.01730.0130.11640.00470.1476-20.8977-1.0005-6.1387
74.2308-1.4667-3.52881.54462.43775.3-0.20260.2401-0.7797-0.37060.20450.49170.8880.06990.18750.4491-0.0004-0.0330.2953-0.06870.2752-28.3385-8.6247-20.4929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 58 )
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 78 )
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 114 )
7X-RAY DIFFRACTION7chain 'A' and (resid 115 through 129 )

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