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- PDB-3iju: Chicken egg white lysozyme by highly ordered APA (Anodic Porous A... -

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Basic information

Entry
Database: PDB / ID: 3iju
TitleChicken egg white lysozyme by highly ordered APA (Anodic Porous Alumina) nanotemplate crystallization method
ComponentsLysozyme C
KeywordsHYDROLASE / Hen Egg White Lysozyme / Allergen / Antimicrobial / Bacteriolytic enzyme / Disulfide bond / Glycosidase
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
Lysozyme - #10 / 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 / Lysozyme-like domain superfamily ...Lysozyme - #10 / 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 / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsPechkova, E. / Tripathi, S.K. / Nicolini, C.
CitationJournal: To be Published
Title: Comparison of lysozyme crystals grown by APA and classical hanging drop method
Authors: Pechkova, E. / Tripathi, S.K. / Nicolini, C.
History
DepositionAug 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.064, 79.064, 37.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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 / Details: Egg / Source: (natural) Gallus gallus (chicken) / Strain: white leghorn / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.05 Å3/Da / Density % sol: 39.91 % / Mosaicity: 0.42 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 0.04N NaOAc/HOAc buffer, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9465 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 31, 2006 / Details: mirror
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9465 Å / Relative weight: 1
ReflectionResolution: 1.6→55.907 Å / Num. obs: 16036 / % possible obs: 98.9 % / Redundancy: 11 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 21.6 / Num. measured all: 176731
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 2.8 / Num. measured all: 26673 / Num. unique all: 2322 / Rsym value: 0.221 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2yvb

2yvb


Resolution: 1.6→21.57 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.265 / WRfactor Rwork: 0.244 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.845 / SU B: 1.762 / SU ML: 0.065 / SU R Cruickshank DPI: 0.116 / SU Rfree: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 803 5 %RANDOM
Rwork0.225 ---
obs0.226 16005 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.53 Å2 / Biso mean: 18.645 Å2 / Biso min: 8.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.6→21.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 81 1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211025
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9031389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.585128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.752350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67115166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.441511
X-RAY DIFFRACTIONr_chiral_restr0.0840.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02794
X-RAY DIFFRACTIONr_nbd_refined0.220.3442
X-RAY DIFFRACTIONr_nbtor_refined0.3090.5703
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.599
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3250.327
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.516
X-RAY DIFFRACTIONr_mcbond_it1.322647
X-RAY DIFFRACTIONr_mcangle_it2.15531008
X-RAY DIFFRACTIONr_scbond_it1.5762445
X-RAY DIFFRACTIONr_scangle_it2.4743381
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 72 -
Rwork0.213 1107 -
all-1179 -
obs--100 %

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