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- PDB-6qwz: HEWL lysozyme, crystallized from KCl solution -

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Basic information

Entry
Database: PDB / ID: 6qwz
TitleHEWL lysozyme, crystallized from KCl solution
ComponentsLysozyme C
KeywordsHYDROLASE
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 / Resolution: 1.35 Å
AuthorsBoikova, A.S. / Dorovatovskii, P.V. / Dyakova, Y.A. / Ilina, K.B. / Kuranova, I.P. / Lazarenko, V.A. / Marchenkova, M.A. / Pisarevsky, Y.V. / Timofeev, V.I. / Kovalchuk, M.V.
CitationJournal: To Be Published
Title: HEWL lysozyme, crystallized from different chlorides
Authors: Boikova, A.S. / Dorovatovskii, P.V. / Dyakova, Y.A. / Ilina, K.B. / Kuranova, I.P. / Lazarenko, V.A. / Marchenkova, M.A. / Pisarevsky, Y.V. / Timofeev, V.I. / Kovalchuk, M.V.
History
DepositionMar 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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)14,5086
Polymers14,3311
Non-polymers1775
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-46 kcal/mol
Surface area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.660, 78.660, 37.061
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-333-

HOH

21A-374-

HOH

31A-406-

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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.80241 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.80241 Å / Relative weight: 1
ReflectionResolution: 1.35→27.81 Å / Num. obs: 26135 / % possible obs: 98.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.4
Reflection shellResolution: 1.35→1.385 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WLD

4wld


Resolution: 1.35→27.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.287 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.065 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21647 1334 5.2 %RANDOM
Rwork0.16797 ---
obs0.17042 24493 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.985 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.35→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 5 134 1139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191037
X-RAY DIFFRACTIONr_bond_other_d0.0020.02947
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9011408
X-RAY DIFFRACTIONr_angle_other_deg1.12932160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9915132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0323.13751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31415168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7641511
X-RAY DIFFRACTIONr_chiral_restr0.1240.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021227
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02274
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_it1.3851.269522
X-RAY DIFFRACTIONr_mcbond_other1.381.267521
X-RAY DIFFRACTIONr_mcangle_it1.7451.915653
X-RAY DIFFRACTIONr_mcangle_other1.7481.917654
X-RAY DIFFRACTIONr_scbond_it1.791.507515
X-RAY DIFFRACTIONr_scbond_other1.7881.508516
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0012.18755
X-RAY DIFFRACTIONr_long_range_B_refined2.61511.7371396
X-RAY DIFFRACTIONr_long_range_B_other2.3911.2891337
X-RAY DIFFRACTIONr_rigid_bond_restr3.39131982
X-RAY DIFFRACTIONr_sphericity_free21.664549
X-RAY DIFFRACTIONr_sphericity_bonded6.21752049
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 92 -
Rwork0.267 1802 -
obs--100 %

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