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- PDB-8d7j: Crystal structure of hen egg white lysozyme at 250 Kelvin -

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Basic information

Entry
Database: PDB / ID: 8d7j
TitleCrystal structure of hen egg white lysozyme at 250 Kelvin
ComponentsLysozyme C
KeywordsHYDROLASE / Antimicrobial / Bacteriolytic enzyme / Glycosidase / Hydrolase.
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRibeiro, F.S. / Lima, L.M.T.R.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Other government1 Brazil
Other government2 Brazil
CitationJournal: Biophys.Chem. / Year: 2023
Title: Linking B-factor and temperature-induced conformational transition.
Authors: de Sa Ribeiro, F. / Lima, L.M.T.R.
History
DepositionJun 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,78711
Polymers14,3311
Non-polymers45510
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.318, 79.318, 37.756
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-340-

HOH

21A-367-

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 / Fragment: lyzozyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 1.2 M NaCl and 100 mM AcONa pH 4.6

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Data collection

DiffractionMean temperature: 250 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.54184 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Nov 4, 2020
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.5→25.1 Å / Num. obs: 19866 / % possible obs: 99.66 % / Redundancy: 1.9 % / CC1/2: 0.758 / Net I/σ(I): 8.34
Reflection shellResolution: 1.5→25.1 Å / Num. unique obs: 19866 / CC1/2: 0.758

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A8Z

3a8z


Resolution: 1.5→25.095 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.141 / SU ML: 0.042 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1909 1014 5.104 %
Rwork0.1644 18852 -
all0.166 --
obs-19866 99.664 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.127 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å20 Å20 Å2
2---0.001 Å20 Å2
3---0.002 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 20 67 1088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121035
X-RAY DIFFRACTIONr_bond_other_d0.0010.018950
X-RAY DIFFRACTIONr_angle_refined_deg1.821.6341399
X-RAY DIFFRACTIONr_angle_other_deg1.6241.5952164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6675128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18520.65661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54315166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9941511
X-RAY DIFFRACTIONr_chiral_restr0.0990.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021210
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02280
X-RAY DIFFRACTIONr_nbd_refined0.2340.2232
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.2891
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2533
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.230
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0980.21
X-RAY DIFFRACTIONr_nbd_other0.120.212
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0570.26
X-RAY DIFFRACTIONr_mcbond_it1.3551.258515
X-RAY DIFFRACTIONr_mcbond_other1.3331.253514
X-RAY DIFFRACTIONr_mcangle_it2.0641.887642
X-RAY DIFFRACTIONr_mcangle_other2.0681.891643
X-RAY DIFFRACTIONr_scbond_it2.8821.73520
X-RAY DIFFRACTIONr_scbond_other2.881.74521
X-RAY DIFFRACTIONr_scangle_it4.4662.418757
X-RAY DIFFRACTIONr_scangle_other4.4632.428758
X-RAY DIFFRACTIONr_lrange_it5.84516.0911227
X-RAY DIFFRACTIONr_lrange_other5.83416.0981225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5370.276760.2441359X-RAY DIFFRACTION98.7612
1.537-1.5790.263850.2081289X-RAY DIFFRACTION98.2833
1.579-1.6250.223700.1831298X-RAY DIFFRACTION99.7812
1.625-1.6750.18730.1741236X-RAY DIFFRACTION99.6954
1.675-1.730.217580.1541252X-RAY DIFFRACTION100
1.73-1.790.16590.1521189X-RAY DIFFRACTION100
1.79-1.8580.267540.1571151X-RAY DIFFRACTION100
1.858-1.9340.189680.1551102X-RAY DIFFRACTION100
1.934-2.0190.166490.1461070X-RAY DIFFRACTION100
2.019-2.1180.181520.151032X-RAY DIFFRACTION100
2.118-2.2320.142520.155975X-RAY DIFFRACTION99.9027
2.232-2.3670.245450.151939X-RAY DIFFRACTION99.8985
2.367-2.530.194580.161855X-RAY DIFFRACTION100
2.53-2.7330.158400.162823X-RAY DIFFRACTION99.7688
2.733-2.9930.146380.187752X-RAY DIFFRACTION100
2.993-3.3450.206290.169703X-RAY DIFFRACTION99.7275
3.345-3.860.178330.166622X-RAY DIFFRACTION100
3.86-4.7220.17350.139528X-RAY DIFFRACTION100
4.722-6.6550.189250.159425X-RAY DIFFRACTION100
6.655-25.0950.273150.191252X-RAY DIFFRACTION95.6989

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