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- PDB-4i8s: Hen Lysozyme protein crystallization via standard hanging drop va... -

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Basic information

Entry
Database: PDB / ID: 4i8s
TitleHen Lysozyme protein crystallization via standard hanging drop vapor diffusion
ComponentsLysozyme C
KeywordsHYDROLASE / thin films / Langmuir-Blodgett / optimal crystallization
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: 2 Å
AuthorsBelmonte, L. / Pechkova, E. / Bragazzi, N. / Scudieri, D. / Nicolini, C.
CitationJournal: To be Published
Title: A review of the strategies for obtaining high quality crystals utilizing nanotechnologies and space
Authors: Pechkova, E. / Bragazzi, N. / Belmonte, L. / Nicolini, C.
History
DepositionDec 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.340, 80.340, 37.160
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-304-

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.: 111 / 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: 2.09 Å3/Da / Density % sol: 41.21 % / Mosaicity: 0.97 °
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 2→56.809 Å / Num. all: 8682 / Num. obs: 8682 / % possible obs: 100 % / Redundancy: 11.5 % / Rsym value: 0.199

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.17 Å40.17 Å
Translation2.17 Å40.17 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.17 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.857 / WRfactor Rfree: 0.2802 / WRfactor Rwork: 0.2128 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8282 / SU B: 4.568 / SU ML: 0.131 / SU R Cruickshank DPI: 0.2162 / SU Rfree: 0.1944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 408 4.7 %RANDOM
Rwork0.1949 ---
obs0.1978 8608 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.87 Å2 / Biso mean: 17.3208 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.53 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 111 1112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211025
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9031389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5262350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24715166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2871511
X-RAY DIFFRACTIONr_chiral_restr0.120.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02794
X-RAY DIFFRACTIONr_mcbond_it1.0531.5635
X-RAY DIFFRACTIONr_mcangle_it1.99321008
X-RAY DIFFRACTIONr_scbond_it3.373390
X-RAY DIFFRACTIONr_scangle_it5.1994.5381
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 39 -
Rwork0.151 590 -
all-629 -
obs--99.06 %

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