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- PDB-6qwy: HEWL lysozyme, crystallized from NaCl solution -

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Basic information

Entry
Database: PDB / ID: 6qwy
TitleHEWL lysozyme, crystallized from NaCl 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5428
Polymers14,3311
Non-polymers2117
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-67 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.147, 77.147, 37.139
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-327-

HOH

21A-332-

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.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.93 Å3/Da / Density % sol: 36.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: NaCl

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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→27.28 Å / Num. obs: 25204 / % possible obs: 99.97 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 16.1
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→27.28 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.893 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 1283 5.1 %RANDOM
Rwork0.15837 ---
obs0.16044 23918 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.242 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.35→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 7 141 1148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191049
X-RAY DIFFRACTIONr_bond_other_d0.0030.02956
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.8971426
X-RAY DIFFRACTIONr_angle_other_deg1.15332179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9265134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47823.26952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42115169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0391511
X-RAY DIFFRACTIONr_chiral_restr0.1450.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021256
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02281
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_it1.0641.092529
X-RAY DIFFRACTIONr_mcbond_other1.0511.092529
X-RAY DIFFRACTIONr_mcangle_it1.3481.65666
X-RAY DIFFRACTIONr_mcangle_other1.3511.653667
X-RAY DIFFRACTIONr_scbond_it1.4191.336519
X-RAY DIFFRACTIONr_scbond_other1.4181.338520
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6141.92761
X-RAY DIFFRACTIONr_long_range_B_refined2.17610.3281418
X-RAY DIFFRACTIONr_long_range_B_other1.9879.8491336
X-RAY DIFFRACTIONr_rigid_bond_restr2.15932003
X-RAY DIFFRACTIONr_sphericity_free19.468542
X-RAY DIFFRACTIONr_sphericity_bonded5.71152086
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 81 -
Rwork0.155 1739 -
obs--100 %

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