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- PDB-9uyr: In situ structure of egg-white lysozyme using a goniometer-compat... -

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Basic information

Entry
Database: PDB / ID: 9uyr
TitleIn situ structure of egg-white lysozyme using a goniometer-compatible chip-based platform
ComponentsLysozyme C
KeywordsHYDROLASE / small protein / hanging-drop crystallization / single crystal / anti-microbial agent / CYTOSOLIC PROTEIN
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 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 bacterium / defense response to Gram-positive bacterium / endoplasmic reticulum / : / 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: 1.59 Å
AuthorsGhosh, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: J.Appl.Crystallogr. / Year: 2026
Title: A user-friendly goniometer-compatible fixed-target platform for macromolecular crystallography at synchrotrons
Authors: Ghosh, S. / Banacore, A. / Norder, P. / Bjelcic, M. / Kabbinale, A. / Nileshwar, P. / Wehlander, G. / de Sanctis, D. / Basu, S. / Orlans, J. / Vallejos, A. / Vallejos, L.M.G. / Neutze, R. / Branden, G.
History
DepositionMay 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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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)14,3903
Polymers14,3311
Non-polymers582
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-18 kcal/mol
Surface area6630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.116, 79.116, 37.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1128-

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: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 40.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 40mg/mL in 50mM sodium acetate, 0.8M NaCl

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.75 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.59→39 Å / Num. obs: 16028 / % possible obs: 95.7 % / Redundancy: 6 % / Biso Wilson estimate: 20.5 Å2 / CC1/2: 0.99 / Net I/σ(I): 16
Reflection shellResolution: 1.59→1.65 Å / Num. unique obs: 1592 / CC1/2: 0.62

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoPROCdata processing
PHENIX1.17.1_3660phasing
PHENIX1.17.1_3660refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→35.38 Å / SU ML: 0.1154 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.3595
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.194 795 4.97 %
Rwork0.1689 15208 -
obs0.1702 16003 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.81 Å2
Refinement stepCycle: LAST / Resolution: 1.59→35.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 0 56 1059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00471021
X-RAY DIFFRACTIONf_angle_d0.7331381
X-RAY DIFFRACTIONf_chiral_restr0.0514144
X-RAY DIFFRACTIONf_plane_restr0.004181
X-RAY DIFFRACTIONf_dihedral_angle_d22.0325143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.690.24811190.23982539X-RAY DIFFRACTION97.51
1.69-1.820.23241280.20842510X-RAY DIFFRACTION96.67
1.82-20.2021350.1762520X-RAY DIFFRACTION96.69
2-2.290.16121290.16262532X-RAY DIFFRACTION96.34
2.29-2.890.21271420.18172501X-RAY DIFFRACTION94.36
2.89-35.380.18261420.15062606X-RAY DIFFRACTION92.84
Refinement TLS params.Method: refined / Origin x: 20.5543845517 Å / Origin y: -0.463937525242 Å / Origin z: 18.7700290258 Å
111213212223313233
T0.137055681837 Å2-0.0154779905028 Å20.0224754378523 Å2-0.108804932758 Å20.00179024918816 Å2--0.132712764983 Å2
L2.99309938398 °2-1.55936042836 °20.231685283273 °2-2.70253705849 °2-0.174197280519 °2--1.49055708916 °2
S0.00476097642548 Å °0.0598324046194 Å °-0.195823711244 Å °-0.00673541384411 Å °-0.0107580932843 Å °0.0647566691892 Å °0.0515275641206 Å °-0.0476468668786 Å °0.000739390838138 Å °
Refinement TLS groupSelection details: all

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