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- PDB-8ya1: HEN EGG WHITE LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 8ya1
TitleHEN EGG WHITE LYSOZYME
ComponentsLysozyme C
KeywordsHYDROLASE / LYSOZYME / HEN EGG WHITE
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: 1.57 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.258, 78.258, 36.808
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-258-

HOH

21A-282-

HOH

31A-335-

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.: 138 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.44 %
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: 100 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 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.924 Å / Relative weight: 1
ReflectionResolution: 1.57→39.13 Å / Num. obs: 16608 / % possible obs: 99.9 % / Redundancy: 18.8 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.013 / Rrim(I) all: 0.057 / Χ2: 1.06 / Net I/σ(I): 30.9 / Num. measured all: 311955
Reflection shellResolution: 1.57→1.59 Å / % possible obs: 97.1 % / Redundancy: 18.2 % / Rmerge(I) obs: 0.639 / Num. measured all: 14320 / Num. unique obs: 788 / CC1/2: 0.94 / Rpim(I) all: 0.152 / Rrim(I) all: 0.658 / Χ2: 0.96 / Net I/σ(I) obs: 5.2

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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: 1.57→39.13 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 1657 10 %
Rwork0.1925 --
obs0.1947 16564 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 138 1139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071021
X-RAY DIFFRACTIONf_angle_d1.1141381
X-RAY DIFFRACTIONf_dihedral_angle_d6.045143
X-RAY DIFFRACTIONf_chiral_restr0.064144
X-RAY DIFFRACTIONf_plane_restr0.01181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.27651320.23691189X-RAY DIFFRACTION98
1.61-1.670.27781370.20551240X-RAY DIFFRACTION100
1.67-1.730.2321340.20941192X-RAY DIFFRACTION100
1.73-1.790.23081360.20931226X-RAY DIFFRACTION100
1.79-1.880.24281350.19971222X-RAY DIFFRACTION100
1.88-1.970.22291370.19531228X-RAY DIFFRACTION100
1.98-2.10.23241360.20091228X-RAY DIFFRACTION100
2.1-2.260.26041380.19021236X-RAY DIFFRACTION100
2.26-2.490.22481390.18721251X-RAY DIFFRACTION100
2.49-2.850.23171390.20441254X-RAY DIFFRACTION100
2.85-3.590.18741430.17791280X-RAY DIFFRACTION100
3.59-39.130.18091510.18791361X-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)
12.9843-0.38470.36162.2674-0.66193.63550.09560.1626-0.3824-0.3187-0.0805-0.08720.31560.46350.01850.25940.03780.00730.2054-0.05010.2244-16.5033-6.7838-18.319
24.7022-0.0891.86941.8289-0.3531.05450.19-0.1555-0.7586-0.0306-0.06970.2310.49830.1005-0.26160.3246-0.0168-0.03150.14840.01860.2491-23.4831-11.4861-7.19
30.9060.5833-0.17870.64530.02890.4627-0.04950.03060.1085-0.05940.04830.0847-0.0157-0.08280.0050.1792-0.0095-0.00380.1538-0.0150.179-21.73580.2952-14.9281
42.62470.1789-0.49982.8896-0.01155.90530.4015-0.16840.8150.12820.185-0.104-0.3685-0.4126-0.32730.23610.01220.05750.2324-0.04930.2587-19.521514.4262-4.2686
51.96180.60860.71942.4962-0.8281.15680.1009-0.27820.10290.2211-0.18120.05790.0076-0.07210.1440.2119-0.02920.01030.2039-0.01670.1716-16.49426.9325-2.1094
60.06350.4612-0.03195.59910.50060.19230.0157-0.3705-0.04420.7549-0.094-0.34310.07370.04670.24150.3452-0.0373-0.04440.30220.0030.225-13.76264.91224.9601
71.03010.78660.17021.2694-0.10050.36050.0208-0.0236-0.2762-0.1094-0.0959-0.26170.16460.23410.02820.21390.01160.00280.18810.01440.2316-13.4468-2.0486-5.8104
82.05180.16691.37882.2964-0.53244.5221-0-0.30160.22010.2951-0.06570.0736-0.6679-0.2938-0.04470.2017-0.00640.00020.1544-0.0170.1823-29.36490.0872-5.2347
94.0958-1.248-1.78592.85581.93524.3992-0.16970.3526-0.6427-0.1224-0.03990.00430.8598-0.1545-0.04160.3968-0.02010.00150.2382-0.0530.2781-28.5938-8.8453-19.5718
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 42 )
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 50 )
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 68 )
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 78 )
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 99 )
8X-RAY DIFFRACTION8chain 'A' and (resid 100 through 114 )
9X-RAY DIFFRACTION9chain 'A' and (resid 115 through 129 )

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