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- PDB-5iel: Structure of Lysozyme labeled with fluorescein isothiocyanate (FI... -

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Basic information

Entry
Database: PDB / ID: 5iel
TitleStructure of Lysozyme labeled with fluorescein isothiocyanate (FITC) at 1.15 Angstroms resolution
ComponentsLysozyme C
KeywordsHYDROLASE / glycoside hydrolase muramidase fluorophore
Function / homology
Function and homology information


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 Gram-positive bacterium / defense response to bacterium ...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 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
Chem-6B9 / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsKachalova, G.S. / Vlaskina, A.V. / Popov, A.P. / Simanovskaia, A.A. / Krukova, M.V. / Lipkin, A.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Fund of Fundamental Reasearch13-04-12084 Russian Federation
CitationJournal: To Be Published
Title: Structure of Lysozyme labeled with fluorescein isothiocyanate (FITC) at 1.15 Angstroms resolution
Authors: Kachalova, G.S. / Vlaskina, A.V. / Popov, A.P. / Simanovskaia, A.A. / Krukova, M.V. / Lipkin, A.V.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

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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)14,7232
Polymers14,3311
Non-polymers3911
Water3,135174
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.756, 80.756, 36.561
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-328-

HOH

21A-404-

HOH

31A-471-

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 / Details: FCZ- fluorophore 5-isothiocyanatofluorescein / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-6B9 / 2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-5-[(E)-(sulfanylmethylidene)amino]benzoic acid


Mass: 391.397 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H13NO5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES 30% v/v Jeffamine ED-2001 ; 0.2M Magnesium nitrate hexahydrate 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97241 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97241 Å / Relative weight: 1
ReflectionResolution: 1.15→57.1 Å / Num. obs: 43530 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/av σ(I): 17.3 / Net I/σ(I): 16.5
Reflection shellResolution: 1.15→1.18 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.76 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NGI

4ngi


Resolution: 1.15→57.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.278 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036
RfactorNum. reflection% reflectionSelection details
Rfree0.17577 2184 5 %RANDOM
Rwork0.14754 ---
obs0.149 41269 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.973 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.15→57.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 28 174 1203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191134
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2651.91557
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2223.01953
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24315180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.521512
X-RAY DIFFRACTIONr_chiral_restr0.1590.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02999
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6971.408557
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0522.123710
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.461.707577
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.65614.8295502
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.23131134
X-RAY DIFFRACTIONr_sphericity_free36.073524
X-RAY DIFFRACTIONr_sphericity_bonded13.88951247
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 155 -
Rwork0.278 3008 -
obs--99.81 %

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